Substrate Recognition by a Colistin Resistance Enzyme from

Apr 9, 2018 - It also demonstrates that ICRMc catalytic domain dimerization is required for substrate binding. ..... Zn2+-free ICRMc was crystallized ...
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Substrate recognition by a colistin resistance enzyme from Moraxella catarrhalis

is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the

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Peter J Stogios, Georgina Cox, Haley L. Zubyk, Elena Evdokimova, Zdzislaw Wawrzak, Gerard D Wright, and Alexei Savchenko

is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the

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ACS Chem. Biol., Just Accepted Manuscript • DOI: 10.1021/ acschembio.8b00116 • Publication Date (Web): 09 Apr 2018 Downloaded from http://pubs.acs.org on April 10, 2018

is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the

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is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the

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is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the

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is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the

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ethical guidelines that apply to the journal pertain. ACS cannot be held res consequences arising from the use of information contained in these “Just A

is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the

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ACS Chemical Biology Page 4 of 35 577

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1

Substrate recognition by a colistin resistance enzyme from Moraxella

2

catarrhalis

3 4 5

Peter J. Stogios1, 2, Georgina Cox3,*, Haley L. Zubyk3, Elena Evdokimova1, 2, Zdzislaw

6

Wawrzak4, Gerard D. Wright3, Alexei Savchenko1,2,5,#

7 8

1

9

Ontario, Canada M5G 1L6

Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto,

10

2

Center for Structural Genomics of Infectious Diseases (CSGID)

11

3

Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for

12

Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1

13

4

14

United States

15

5

16

Health Research Innovation Centre, 3330 Hospital Drive NW, HRIC-2C66, Calgary, Alberta,

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T2N 4N1

LS-CAT, Synchrotron Research Center, Northwestern University, Argonne, Illinois 60439,

Department of Microbiology, Immunology and Infectious Diseases, University of Calgary,

18 19 20

*Current address: Department of Molecular and Cellular Biology, University of Guelph,

21

Guelph, Ontario, Canada N1G 2W1

22

#

23

210-7980.

Corresponding author: Alexei Savchenko. Email: alexei.savchenko@ucalgary.ca Tel: (403)

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Abstract

25

Lipid A phosphoethanolamine (PEtN) transferases render bacteria resistant to the last resort

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antibiotic colistin. The recent discoveries of pathogenic bacteria harboring plasmid-borne PEtN

27

transferases (mcr) genes have illustrated the serious potential for wide dissemination of these

28

resistance elements.

29

environmental niches with Enterobacteriaceae. Here, we describe the crystal structure of the

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catalytic domain of the chromosomally-encoded colistin resistance PEtN transferase, ICRMc (for

31

intrinsic colistin resistance) of Moraxella catarrhalis. The ICRMc structure in complex with

32

PEtN reveals key molecular details including specific residues involved in catalysis and PEtN

33

binding. It also demonstrates that ICRMc catalytic domain dimerization is required for substrate

34

binding. Our structure-guided phylogenetic analysis provides sequence signatures defining

35

potentially colistin-active representatives in this enzyme family. Combined, these results advance

36

the molecular and mechanistic understanding of PEtN transferases and illuminate their origins.

The origin of mcr-1 is traced to Moraxella species co-occupying

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Introduction

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The polymyxin antibiotic colistin is classified as an antibiotic of critical importance by

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the World Health Organization due to its activity against multi-drug resistant Gram-negative

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pathogens 1. Colistin is utilized as a treatment of last resort for recalcitrant infections such as

41

those caused by carbapenem-resistant Enterobacteriaceae. Even though colistin is nephrotoxic,

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the seriousness of such infections and the dearth of alternative treatments has increasingly

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secured a place for this antibiotic in the infectious disease treatment armory in the absence of

44

new antibiotics 2.

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Many species are intrinsically-resistant to polymyxins, including Neisseria meningitidis, 3,4

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Helicobacter pylori, Burkholderia cepacia and Moraxella catarrhalis

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resistance harbored by these bacteria include expression of efflux pumps, shedding of capsule

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polysaccharide and modification of lipopolysaccharide (LPS), the latter of which appears the

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most prevalent (reviewed in 5). Diverse covalent modifications of LPS, which include among

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others the addition of phosphoethanolamine (PEtN) groups (reviewed in 6) are thought to alter

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the physical properties of the outer membrane, resulting in polymyxin resistance. The increased

52

clinical and agricultural use of colistin has been linked to the mobilization and transfer of colistin

53

resistance elements to human pathogenic bacteria such as Escherichia coli, Klebsiella

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pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii, representing serious

55

threats to the effectiveness of polymyxins against these species 3.

. The mechanisms of

56

Well-characterized representatives of PEtN transferases include EptA from E. coli, V.

57

cholerae and H. pylori, EptA (originally named LptA) from N. meningitidis, PmrC from A.

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baumannii and CptA from Campylobacter jejuni (reviewed in 6). These chromosomally-encoded

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enzymes catalyze the transfer of PEtN from phosphatidylethanolamine (PE) onto the lipid A

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moiety of LPS. E. coli EptB is another type of PEtN transferase which specifically catalyzes the

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modification of the outer 3-deoxy-D-manno-octulosonic acid (Kdo) residue of LPS 7.

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The recent discovery of the PEtN transferase encoded by the mcr-1 gene 8 mobilized on a

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plasmid raised the possibility of accelerated dissemination and acquisition of colistin resistance

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among pathogens and/or its collection into multi-drug resistance cassettes 9. Indeed, this gene

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has since been detected in other Enterobacteriaceae species around the world, in additional

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patient isolates and in retrospective searches of culture collections

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found on mobile genetic elements containing up to nine other antibiotic resistance genes,

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including extended-spectrum β-lactamases (ESBLs)

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mobilization of colistin resistance, additional genes encoding PEtN transferases including mcr-2,

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which shares 81% sequence identity with mcr-1, plus the more sequence-distinct mcr-3, mcr-4

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and mcr-5 have been recently discovered on Enterobacteriaceae plasmids

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transferases have mobilized multiple times and thus are becoming worrisome resistance

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determinants that may have serious and long-lasting clinical implications.

10,14,18

.

10-17

. mcr-1 has also been

As further evidence of the

19-21

. Thus, PEtN

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Resistance genes manifesting in the clinic can often be traced to environmental and other

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bacteria which represent a global reservoir of resistance genes that can be transferred between

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diverse genera via mobile genetic elements (reviewed in

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clinical levels of antibiotic resistance such as qnrA and blaCTX-M were subsequently traced to

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aquatic bacteria (reviewed in

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suggested for mcr-1 and similar PEtN transferase genes. Sequence similarity searches identify

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close MCR-1 and MCR-2 orthologs (61-65% identity of the full-length protein sequences) in the

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Moraxellaceae family, specifically in the human pathogen Moraxella catarrhalis, the nematode

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symbiont Moraxella osloensis, and the environmental bacteria Enhydrobacter aerosaccus and

24

).

22,23

). For example, genes conferring

Along the same lines, environmental paralogues were

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Psychrobacter spp. 8. Based on these observations, it was suggested that Moraxella species

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occupying the same ecological niche as E. coli encode the ancestral gene of mcr-1 and mcr-2 19;

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a subsequent study indeed detected mcr-1 orthologous genes in numerous Moraxella species

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Thus, Moraxella or related species may represent an ecological reservoir for mobilization of

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PEtN transferases to other pathogens; however, the molecular and functional characterization of

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these ancestral MCR-1 proteins has been lacking.

25

.

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According to sequence analysis, PEtN transferases are comprised of an N-terminal

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transmembrane region and a periplasm-facing C-terminal hydrolase domain belonging to the

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alkaline phosphatase superfamily. The periplasmic catalytic domains of MCR-1, MCR-2, EptA

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and EptC have been recently structurally characterized. Some of the revealed common molecular

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features observed in the active site of these enzymes included a conserved catalytic threonine

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(often covalently linked to phosphate) and multiple Zn2+ binding sites

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structures of PEtN catalytic domains also featured disulfide bridges between spatially co-

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localized cysteine residues. These structural data provided the molecular framework for

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understanding of PEtN transferases, however, the molecular information concerning substrate

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recognition is still lacking. Furthermore, significant sequence divergence between EptA and

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EptC and MCR-1 (EptA and EptC both share only 42% of sequence identity to MCR-1 in the

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catalytic domain) necessitates further structural and functional studies into closer representatives

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of the latter enzyme to define the possible role of these enzymes in development of colistin

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resistance.

26-33

.

The crystal

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In this study, we characterized the crystal structure of the catalytic domain of the PEtN

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transferase from M. catarrhalis (which we designate as ICRMc), the protein that represents the

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closest known ortholog to MCR-1 and MCR-2 and is responsible for intrinsic colistin resistance

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of this bacterium. Our crystal structures also provide insights into the molecular basis of

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recognition of the PEtN substrate and identify a putative role of dimerization for resistance

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activity.

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characteristics in their catalytic domains, supporting the hypothesis that Moraxellaceae are the

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environmental reservoir of PEtN transferases.

Our findings show that MCR-1 and ICRMc share key structural and functional

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Results and Discussion

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icrMc confers polymyxin resistance

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To test the ability of ICRMc to confer the resistance we expressed icrMc in E. coli

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BW25113 and compared its ability to grow in the presence of colistin and polymyxin B with that

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of the same E. coli strain expressing mcr-1. Both the icrMc and mcr-1 expressing strains showed

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4 to 16 fold (depending on promoter strength/expression level

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antibiotics compared to the E. coli strain with no expression vector (Table 1). Next we tested

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whether the expression of the icrMc or mcr-1 fragments corresponding to the PEtN transferase

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periplasmic catalytic domain (designed icrMccat and mcr-1cat) in the same E. coli strain is

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sufficient to confer polymyxin resistance. The results showed that E. coli harboring icrMccat or

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mcr-1cat did not show a polymyxin resistance phenotype. These results demonstrated that

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expression of icrMc confers polymyxin resistance comparable to that of mcr-1 and that both

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enzymes require their N-terminal transmembrane regions to confer drug resistance in the cell.

34

) higher resistance to these

125 126

MCR-1, MCR-2 and ICRMc define a distinct group in the broader PEtN transferase family

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To clarify the phylogenetic relationship between ICRMc and other PEtN transferases, we

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performed a phylogenetic reconstruction of the PEtN transferase family, including 89 known

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MCR and related proteins (Figure 1). This analysis revealed five clades which segregate along

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their substrate specificity. One of the clades is represented by MCR-3, MCR-4 and EptA, known

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to catalyze transfer PEtN from PE to lipid A. The second one features orthologs of MCR-5 found

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in Legionella species. The third clade is represented by EptB, which acts on Kdo, while the

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fourth clade includes EptC/CptA, which target lipid A. The fifth clade contains orthologs of

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MCR-1 and MCR-2, which we termed as MCR-1-like.

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divergence reflected in low amino acid sequence similarity between representatives of different

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clades. Specifically, EptB and MCR-3 shared only 25% and 32% of sequence identity with

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MCR-1. Within the MCR-3/MCR-4/EptA clade, the MCR-3 and MCR-4 enzymes appear to be

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distinct from the rest of their orthologs, suggesting separate evolutionary paths or ancestral

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origins. These observations are consistent with multiple incidents of mobilization of intrinsic

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PEtN ancestral genes leading to diversification among members of this family and reflecting

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different functional properties. Consistent with previous reports

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MCR-1-like

clade

contains

a

8,25

The five clades show significant

, our phylogenetic reconstruction recapitulated that

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the

closely

associated

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Gammaproteobacteria that share between 57 and 98% of sequence identity with MCR-1,

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including MCR-1, MCR-2 and members in Moraxellaceae species: ICRMc, ICRM.

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ICRE .aerosaccus. Beyond this group, the MCR-1-like clade contained a group of uncharacterized

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proteins, including representatives from Sulfurospirillum spp., Arcobacter spp., Campylobacter

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sputurum and Marinobacter subterrani and these share between 41 and 79% identity with MCR-

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1. Notably, this group also shares significant similarity with the EptA clade. These observations

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indicate that the ability to confer colistin resistance established for MCR-1 and ICRMc may be

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group

of

sequences

from

osloensis

and

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shared by the wider sequence-related group of PEtN transferases, which forms a distinct clade in

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the PEtN transferase superfamily.

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Alignment of PEtN transferase sequences (Figure S1) revealed higher degree of sequence

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conservation in the C-terminal region and (i.e. 68% sequence identity between ICRMc and MCR-

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1 or MCR-2). Combined with the comparable resistance phenotype conferred by expression of

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these enzymes, this points to strong conservation of functional and structural features between

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the ICRMc and MCR-1/MCR-2 enzymes.

158 159

Crystal structure of the catalytic domain of ICRMc

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Next, we purified and crystallized the catalytic domain of ICRMc (ICRMccat) spanning

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residues 235 to 578 (Figure 2A). The crystal structure of this domain was determined to 2.61 Å

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by Molecular Replacement using the structure of N. meningitis EptA/LptA 26 as a model. The x-

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ray crystallographic statistics are summarized in Table 2.

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The crystal structure contains one copy of the ICRMccat domain in the asymmetric unit.

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Residues 244 through 578 could be traced in the electron density, while residues 235-243 appear

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disordered.

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characterized by a central seven-stranded β-sheet mainly parallel in topology, with the edge

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strand β12 oriented in an anti-parallel orientation (Figure 2A).

The resolved ICRMccat residues adopted the common sulfatase/hydrolase fold,

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The structure of ICRMccat reveals two unambiguous disulfide bonds (Cys390 to Cys398,

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Cys448 to Cys456). Another pair of cysteine residues, Cys311 and Cys321 appear reduced,

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however the proximity of their side chains suggests the possibility of formation of an additional

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disulfide bond (Figure 2A). We interpreted additional difference electron density in the structure

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as six sulfate and one phosphate ions. Unexpectedly, the ICRMccat crystal structure did not

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contain additional electron density corresponding to the expected Zn2+ ion required for PEtN

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transferases

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ICRMccat purification, we soaked ICRMccat protein crystals in zinc chloride-supplemented buffer

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(see Methods for details). We detected significant anomalous diffraction at the Zn2+ dispersion

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absorption peak for such crystals and identified additional electron density corresponding to a

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single Zn2+ atom bound to ICRMccat active site (Figure 2A, Figure 3).

26,27,29-33

. Interpreting this as possible depletion of Zn2+ ions in the course of

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The active site region of the ICRMccat localized to a small (~200 Å3) pocket at the “top”

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of the central β-sheet (as shown in Figure 2B) lined by residues from converging loops. This

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pocket was on the large, flat face of the ICRMccat domain close to its N-terminus. Apart from the

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Zn2+, the active site contains a phosphate ion at 3.7 Å distance from the Zn2+, which is anchored

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by a network of interactions with the active site residues (Figure 3). The Zn2+ ion is coordinated

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primarily by the side chains of Glu273, Thr315, Asp498 and His499. The phosphate forms

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interactions with the sidechain hydroxyl and backbone amide of Thr315, the sidechain of His511

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and two ordered water molecules, one of which also interacted with the Zn2+ ion. The Zn2+ and

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phosphate-binding residues are in turn oriented by a network of interactions with other active site

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residues including Asn359, Ser360 and His424. Notably, Thr315 in the ICRMccat active site

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occupies the position corresponding to the phosphate-accepting nucleophilic residue in the other

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PEtN transferases26,27,29-32. Analysis of ICRMccat residues interacting with both Zn2+ and the

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phosphate ions also highlights His429 as a functionally important residue, although its

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interaction with the Zn2+ was mediated through a hydrogen bond with the coordinated water

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molecule. In addition to the Zn2+ and phosphate ions, the ICRMccat active site contained a sulfate

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ion positioned at 11 Å distance from the phosphate ion described above. The sulfate forms close

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interactions with Arg436, which in turn forms a salt bridge with Glu397. In total, our analysis

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suggested that at least eighteen ICRMc active site residues participate in interactions with the

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Zn2+, phosphate and/or sulfate ligands.

199 200

Substrate recognition requires the dimerization of the ICRMccat domain

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To characterize the molecular basis of substrate recognition by ICRMccat, we crystallized

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Thr315Ala ICRMccat variant in the presence of the disaccharide head-group of lipid A or PEtN, a

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component of the lipid substrate phosphatidylethanolamine.

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nucleophilic residue that attacks the substrate phosphate group. Consistent with this prediction,

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mutation to Ala abolishes antibiotic resitance activity (Table 1). This crystal structure was

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determined to 1.64 Å (Table 2) and revealed a different unit cell and packing compared to the

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wild type ICRMccat. In contrast to the ICRMccat apo structure, the ICRMccatThr315Ala•PEtN

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complex structure features two ICRMccatThr315Ala molecules associated as a homodimer with

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~1190 Å2 buried at the dimerization interface. The ICRMccat protein chains in the PEtN complex

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structure associate in a symmetrical “front-to-front” orientation, with the two active sites facing

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each other (Figure 4A, 4B). Dimerization involves interactions between 38 residues in each

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monomer and impacts both the shape and accessibility of the active sites. In the ICRMccat dimer

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the entrance to the catalytic centers is buried along the dimerization interface with access through

214

deep clefts formed by this interface (Figure 4C). Consistent with this observed association of

215

ICRMccat domains, we also detected the formation of a dimer in solution by size exclusion

216

chromatography, which is more prominent in the presence of Zn2+ ions (Figure S2).

Thr315 is predicted to be the

217

Well-defined additional electron density allowed unambiguous positioning of one PEtN

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molecule in each active site of the ICRMccatThr315Ala dimer in the complex structure (Figure 5).

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The phosphate of PEtN molecule forms interactions with the Zn2+ ion and the side chain of

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His511, as well with the backbone of Ala315 and three water molecules. Intriguingly, the Tyr338

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from the partner monomer chain also contributes to coordination of the substrate molecule

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(Figure 5). Notably, the position of the phosphate group of PEtN molecule in the complex

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structure corresponds to the position of the phosphate ion in the apo-structure. Orientation of the

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PEtN molecule in the ICRMccat active site is consistent with the predicted catalytic mechanism of

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this family whereby a threonine residue (Thr315 in ICRMc) performs nucleophilic attack on the

226

phosphate atom of the phosphatidylethanolamine substrate to generate a phosphoethanolamine –

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Thr intermediate species. We did not observe any interactions between the ethanolamine moiety

228

of PEtN and the enzyme. Taken together, the structural analysis of the ICRMccatThr315Ala• PEtN

229

complex suggests that dimerization of this domain may facilitate the coordination of the

230

substrate providing an additional interaction partner (Tyr338) from adjacent monomer that may

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be required for optimal positioning of the phosphatidylethanolamine substrate for catalysis.

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One of the tested ICRMccatThr315Ala crystals obtained in the presence of lipid A head-group

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lacked the additional density corresponding to the substrate molecule but featured a second Zn2+

234

ion (Zn2 in Figure S3) in the active sites of the ICRMccat dimer.

235

corresponds to that of the phosphate of PEtN in complex structure. In this structure, the Zn2 is

236

coordinated by side chains of residues Glu273, His429 and His511 and the backbone amide of

237

Ala315. In this interaction, the His429 underwent a rotamer change relative to its position in the

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ICRMc apo-structure. Thus there could be an interplay between the binding of a second Zn2+

239

atom and the phosphate groups of the enzyme’s substrates. Furthermore, the active sites of

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ICRMccatThr315Ala•di-Zn2+ structure contain elongated difference electron density corresponding to

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a polyethylene glycol molecule present in the crystallization solution (Figure S3). The position of

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this molecule in the active site approaches the catalytic center of the enzyme and forms a packing

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interaction against His429 and hydrophobic interactions with Met426 and the aliphatic region of

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the Lys378 sidechain. Accordingly, we propose that the position of the polyethylene glycol

245

molecule may be indicative of the position of the lipid A head-group in the ICRMccat active site.

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Guided by our structural analysis, we tested the roles of ICRMccat residues implicated in

247

interactions with Zn2+ and PEtN by site-directed mutagenesis. Residues Thr315, His429, Arg436

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and Tyr338 were individually mutated to Ala in the context of the full-length ICRMc protein. The

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E. coli strains expressing the corresponding ICRMc variants completely lost resistance to colistin

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and polymyxin B compared to the strain carrying the wild type enzyme, confirming the

251

important role of these residues for ICRMc activity (Table 1). Based on these results we postulate

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that coordination of Zn2+ binding by Thr315, His429, Tyr338 residues and unexpectedly,

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interactions of residues Tyr338 and Arg436 with substrate molecules as facilitated by ICRMccat

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domain dimerization, may be essential for the catalytic activity of ICRMc.

255 256

Comparative structural analysis highlights signature active site features of the PEtN

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transferase family

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We conducted a comparative analysis of this structure versus those of recently

259

characterized MCR-1 and MCR-2 resistance enzymes as well as the structures of previously

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characterized EptA and EptC to clarify the shared and distinct features of these PEtN

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transferases.

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The ICRMc structure superimposes with that of MCR-1 and MCR-2 with RMSD of 0.5 Å

263

and 0.5 Å over 251 and 270 matching Cα atoms, respectively (Figure 6). This superimposition

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reveals only minor structural differences primarily in conformations of the β5-η4 and β6-η5

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loops. More importantly, all 18 residues of the active site (Figure 6) are absolutely conserved

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across these three enzymes. Furthermore, these 18 amino acids, which includes the histidine

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(His429) residue undergoing rotation between binding to PEtN or Zn2+ ion in ICRMc structures,

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are universally conserved across the MCR-1-like PEtN transferases (Figure S1). Interestingly,

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the Tyr338 residue, whose role in PEtN binding is facilitated by catalytic domain dimerization, is

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also conserved in the orthologs of ICRMc, MCR-1 and MCR-2. This observation prompted us to

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suggest that the active site architecture, binding mode of PEtN, and coordination of substrates

272

across a dimer interface as visualized in the ICRMc cat-PEtN complex structure is conserved

273

across the MCR-1-like clade of PEtN transferases defined above.

274

Expanding our structure-based sequence analysis to the recently-identified MCR-3,

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MCR-4 and MCR-5 enzymes revealed conservation of 12 out of 18 active site residues

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invariable in MCR-1-like enzymes (Figure S1). These include residues involved in coordination

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of the Zn2+ ion and in catalysis. Notably, we were not able to identify the equivalent of ICRMccat

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residue Tyr338 in MCR-3 or MCR-4. These differences may be indicative of deviation in

279

substrate-binding mode between MCR-1-like PEtN transferases and the MCR-3, MCR-4 and

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MCR-5 enzymes.

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Detailed comparative analysis of ICRMc and EptA and EptC revealed differences in the

282

conformations of the β5-η4 and β6-η5 loops and in active site composition (Figure S4). Of the

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18 active site residues in MCR-1-like enzymes described above, only 11 are conserved in EptA

284

and EptC (Figures S1 and S4). Once again, the conserved residues in EptA and EptC active sites

285

cluster to the Zn2+ binding sites, consistent with a common catalytic mechanism shared across

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the entire PEtN transferase family. In contrast, the four non-conserved residues corresponding to

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ICRMc residues Asn359, Ser360, Lys378 and Met426 cluster together and away from the Zn2+

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binding site. Identification of these subtle differences may be reflective of EptA and EptC

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deviating in substrate preference from MCR-1-like enzymes.

290

Our observation that the dimeric state of ICRMccatThr315Ala forms a solvent-occluded

291

pocket containing a PEG molecule suggests that only in the dimer state of the catalytic domain,

292

or in the context of the full-length protein containing the transmembrane region, is the protein

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capable of forming an active site structure that can recognize the larger lipid A substrate. Indeed,

294

analysis of the crystal structure of EptA, the MCR-1 ortholog from N. meningitidis, suggested

295

that the membrane-spanning portion and the linker to the catalytic domain are involved in

296

mediating substrate interactions35. The detergent (DDM) molecule trapped in the membrane-

297

spanning portion of EptA is oriented toward the active site of the catalytic domain suggesting it

298

mimicks the position of enzyme’s substrate (Figure 7). With our ICRMccatThr315Ala•PEtN crystal

299

structure in hand, we are able to posit a model of the ternary complex with a lipid positioned to

300

attack the phosphoethanolamine-threonine intermediate (Figure 7). This model was developed

301

through a superposition of the structures of EptA•DDM and ICRMccatThr315Ala•PEtN which

302

showed that the position of these two ligands do not overlap: more specifically, the O3B of

303

DDM and O3 of PEtN approached each other in this model and thus this overlay can be used to

304

interpret the position of a phosphorylated lipid molecule in the active site (Figure 7). This model

305

also validates the prediction that EptA Glu114 interacts with the amine group of PEtN 35 as this

306

residue and its equivalent in ICRMc (E113) is positioned within bonding distance to this

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functional group. Consistent with its functional importance, this glutamate residue is conserved

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throughout the PEtN transferase family (except for the EptB subgroup), suggesting it plays a role

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in discrimination for PE. Further structural and enzymatic studies into PEtN transferase and

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their interactions with native substrates are required to further validate this model and reveal

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additional key details.

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The binding of substrates may require the ICRMccat domain’s dimerization which

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according to our structural analysis provides additional interaction partners for the substrate

314

molecules in both actives sites of the dimer. A molecular dynamics simulation of EptA

315

showed that the soluble domain can adopt multiple conformations and “roll” over the simulated

316

membrane surface, indicating that the dimerization interface we observed in ICRMc complex

317

structure may be accommodated in such a fluid situation.

35

318

Our demonstration of the conservation of the molecular details of the ICRMc, MCR-1 and

319

MCR-2 active sites supports the notion that Moraxella species form the reservoir of at least this

320

group of PEtN transferases. This stresses that structural and functional studies of intrinsic

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resistance enzymes in species co-habitating environmental niches as human pathogens are key

322

components of developing a better understanding of the origins and mechanisms of resistance

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impacting clinical management of pathogens. As has been evidenced in numerous examples,

324

and even in the ongoing discovery of new mcr genes, the source of clinical antibiotic resistance

325

is the environment. Progress towards developing a complete understanding of the broader

326

resistome, such as our characterization of ICRMc, is a key component of resistance surveillance

327

and anticipation of future mobilization events.

328

Finally, our structure-based phylogenetic analysis provides a foundational organization of

329

PEtN transferases that clearly shows that these enzymes are diverse in sequence and each

330

discovery of novel mcr genes identifies founding members of subclasses of PEtN transferases.

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This phenomenon parallels the expansion of β-lactamase families over the course of decades of

332

β-lactam clinical deployment

36

and underscores the extent of the dissemination of polymyxin

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resistance. As with β-lactamase family-specific properties, functional insights into individual

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PEtN transferases may not be conserved across the subgroups.

335

structural and molecular diversity of MCR enzymes is critical for drug discovery efforts against

336

these enzymes.

Thus, appreciation of the

337 338

Acknowledgements

339

We thank R. Di Leo for cloning. The structures presented were solved by the Center for

340

Structural Genomics of Infectious Diseases (CSGID, http://csgid.org); this project has been

341

funded in whole or in part with U.S. Federal funds from the National Institute of Allergy and

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Infectious Diseases, National Institutes of Health, Department of Health and Human Services,

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under Contract Numbers HHSN272201200026C and HHSN272201700060C. This research

344

was supported by the Ontario Research Fund Research Excellence (ORF-RE) grant #RE07-048

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(to G.D. Wright and A. Savchenko). This research was also supported by a Canadian Institutes of

346

Health Research grant (FRN-148463) and by a Canada Research Chair in Antibiotic

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Biochemistry (to G.D. Wright).

348 349

References

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Figure Legends

490 491

Figure 1. Phylogenetic relationships of PEtN transferases. The four major clades are

492

independently colored and labeled. Nodes are labeled by Bayesian probability. Arrow labels

493

ICRMc sequence. Protein sequences with an assigned name are labeled with the name plus

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originating species in superscript initials, those proteins identified in mobile elements are labeled

495

with the protein name only. Protein sequences without an assigned name are indicated only with

496

the species name.

497

498

Figure 2. Structure of ICRMc•mono-Zn2+ complex. A) Domain architecture, with termini of

499

the TM and catalytic domains indicated. B) Overall structure. Secondary structure elements are

500

labeled, active site sulfate, phosphate molecules and amino acids are shown in sticks, Zn2+ ion as

501

a black sphere, and cysteines / disulfide bonds with yellow sticks. C) Electrostatic surface

502

representation. Scale of colors is from red = -10 kB/T, white = 0, blue = +10. N-terminus of this

503

domain (residue 243) is labeled.

504

molecules. Dashed black line indicates active site cleft.

Sticks are shown for active site phosphate and sulfate

505 506

Figure 3. Active site of ICRMc•mono-Zn2+ complex. The Zn2+ ion is shown as a grey sphere

507

with purple electron density (anomalous difference map contoured at 20 σ), sulfate electron

508

density is Fo-Fc difference map contoured at 5 σ. Dashes indicate hydrogen bonds or salt bridge

509

interactions. Water molecules are shown as red spheres. The distance between the Zn2+ ion and

510

sulfate ion is indicated.

511 512

Figure 4. Structure of dimeric ICRMccatThr315Ala•mono-Zn2+•PEtN complex. A) Two chains

513

are independently coloured. Zn2+ shown in grey spheres, PEtN shown in green ball-and-stick. B)

514

Surface representation. Two entry paths to active sites are labeled. White shading indicates

515

residues in active site clefts. Bottom view is rotated 90° from the top view in the plane of the

516

page and cut-away for visualization into the solvent-occluded active sites.

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517 518

Figure 5. Active site of dimeric ICRMccatThr315Ala•mono-Zn2+•PEtN complex. A) Same view

519

is shown as in Figure 3. Residues coloured light green are from the partner chain in the dimer.

520

The Zn2+ ion is shown as a grey sphere with anomalous difference density contoured at 20 σ.

521

PEtN is shown in ball-and-stick with Fo-Fc difference density contoured at 3.0 σ. Dashes indicate

522

hydrogen bonds or salt bridge interactions. Water molecules are shown as red spheres. B)

523

Schematic of Zn2+ (shown as Zn1) and PEtN recognition by ICRMccatThr315Ala.

524 525

Figure 6. Comparison of structures of ICRMc, MCR-1 and MCR-2 catalytic domains. Left =

526

overall superposition of the three structures, ICRMc shown in pink, MCR-1 in light blue, MCR-2

527

in orange. Zoom = active site residues. Parenthesis indicate mutation A315 in ICRMc , asterisks

528

indicate Y308 from MCR-1 and MCR-2 are not shown as their crystal structures were not

529

dimeric. PEtN as bound to ICRMccatThr315Ala is shown in green sticks.

530 531

Figure 7. Model of full-length ICRMc•mono-Zn2+•PEtN complex based on the structure of

532

N. meningitidis EptA.

533

Left = overall structures, with ICRMc shown in dark red and EptA in shades of green. DDM as

534

bound to EptA and PEtN as bound to ICRMc are shown in black and green ball-and-stick,

535

respectively. Dashed lines = putative plane of inner membrane. Right = zoom of active site.

536

Residues interacting with Zn2+, DDM or PEtN are shown in sticks and labeled. Double-ended

537

arrow indicates close approach of E114/E143 with amine group of PEtN. Box indicates overlap

538

in spatial position of DDM O3B and PEtN O3 atoms. BH = base helix; PH2 and PH2’ =

539

periplasmic helices 2 and 2’ (nomenclature from 35).

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Page 30 of 35

540 541

Tables

542

Table 1. Heterologous polymyxin resistance conferred by icrMc and mcr-1.

543 Gene None

icrMc

mcr-1

Construct None None pGDP1::icrMc pGDP2::icrMc pGDP1::icrMcThr315Ala pGDP1::icrMcTyr338Arg pGDP1::icrMcHis429Ala pGDP1::icrMcArg436Ala pGDP1::icrMccat pGDP2::icrMccat pGDP1::icrMc pGDP2::icrMc pGDP1::icrMcThr315Ala pGDP1::icrMcTyr338Arg pGDP1::icrMcHis429Ala pGDP1::icrMcArg436Ala pGDP1::icrMccat pGDP2::icrMccat pGDP1::mcr-1 pGDP2::mcr-1 pGDP1::mcr-1cat pGDP2::mcr-1cat pGDP1::mcr-1 pGDP2::mcr-1 pGDP1::mcr-1cat pGDP2::mcr-1cat

Antibiotic Colistin Polymyxin B

Colistin

Polymyxin B

Colistin

Polymyxin B

MIC (µg/mL) 0.25 0.25 2 1 0.25 0.25 0.25 0.25 0.25 0.25 2 1 0.25 0.25 0.25 0.25 0.25 0.25 4 4 N.D. 0.25 4 4 N.D. 0.5

544

Susceptibility testing was performed with E. coli BW25113; pGDP1 = Pbla promoter; pGDP2 =

545

Plac promoter. N.D. = no data.

546 547

Table 2. X-ray diffraction data collection and refinement statistics

548 Structure

ICRMc•PO4 complex

ICRMc•mono-Zn2+ complex

ICRMc Thr315Ala•diZn2+•PEG complex

PDB Code

6BNE

6BNF

6BNC

ICRMc Thr315Ala•monoZn2+•PEtN complex 6BND

Data collection Space group

P4132

P4132

P21212

P21212

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549 550 551 552 553 554 555

ACS Chemical Biology

Structure

ICRMc•PO4 complex

ICRMc•mono-Zn2+ complex

ICRMc Thr315Ala•diZn2+•PEG complex

PDB Code Cell dimensions a=b=c (Å) Resolution, Å Rmergea Rpim CC1/2 I / σ(I) Completeness, % Redundancy

6BNE

6BNF

6BNC

ICRMc Thr315Ala•monoZn2+•PEtN complex 6BND

147.52 104.32 – 2.61 0.181 (3.313)b 0.028 (0.515) 0.840 24.7 (2.6) 100 (100) 77.3 (79.5)

148.27 104.84 – 2.33 0.161 (3.941) 0.025 (0.672) 0.841 24.0 (2.0) 100 (100) 76.5 (66.5)

74.05, 154.25, 66.39 30.00 – 1.50 0.088 (0.595) 0.026 (0.203) 0.982 30.68 (4.1) 99.9 (100) 11.9 (8.8)

74.52, 155.24, 66.41 31.80 – 1.64 0.108 (1.950) 0.044 (0.827) 0.594 14.5 (1.3) 100 (100) 13.4 (12.6)

Refinement Resolution, Å 60.23 – 2.61 46.88 – 2.33 29.82 – 1.50 31.81 – 1.64 No. of unique 16528, 830 23489, 2163 121223, 10848 94685, 3840 reflections: working, test R-factor/free R23.6/27.1 (48.0/48.7) 20.9/24.8 (40.8/46.4) 13.2/15.3 (19.8/23.4) 15.1/19.2 (34.2/32.7) factorc No. of refined atoms, molecules 5293 5255 Protein 2602 2607 2 Zinc N/A 1 4 Phosphate* 5 5 N/A N/A 5 5 N/A N/A Sulfate* N/A N/A 16 PEtN N/A 37 20 42 103 Other solvent 209 1093 1128 Water 116 B-factors Protein 79.1 67.8 17.3 26.9 Zinc N/A 63.8 11.2 26.9 Phosphate* 108.0 82.0 N/A N/A Sulfate* 87.6 78.6 N/A N/A PEtN N/A N/A N/A 29.1 Other solvent 116.2 95.0 29.3 22.9 Water 65.44 66.6 36.2 46.2 r.m.s.d. Bond lengths, Å 0.006 0.002 0.017 0.006 1.380 1.274 1.468 1.319 Bond angles, ° a Rmerge = ΣhΣi|Ii(h) - 〈I(h)〉/ΣhΣiIi(h), where Ii(h) and 〈I(h)〉 are the ith and mean measurement of the intensity of reflection h. b Figures in parentheses indicate the values for the highest resolution shells of the data. c R-factor = Σ|Fpobs – Fpcalc|/ΣFpobs, where Fpobs and Fpcalc are the observed and calculated structure factor amplitudes, respectively. * = molecules in the active site cleft.

556

Methods

557

MIC determination

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Page 32 of 35

558

Full-length icrMc and its catalytic domain (icrMccat; residues 235-578) plus full-length E.

559

coli mcr-1 and its catalytic domain (mcr-1cat; residues 208-541) were ligated into the pGDP1

560

and pGDP2 vectors (in house derivatives of the pBR322 vector; New England BioLabs). These

561

plasmids utilize constitutive promoters of differing strength; the stronger β-lactamase Pbla

562

promoter (pGDP1) and the weaker Plac promoter (pGDP2). Amino acid substitutions in icrMc

563

were performed using Phusion High-Fidelity DNA Polymerase (Thermo Scientific) and the

564

pGDP1:icrMC construct. Constructs were confirmed by sequencing (Central MOBIX facility,

565

McMaster University). Susceptibility testing (in triplicate, with two biological replicates) was

566

performed with E. coli BW25113 cultured in Mueller-Hinton II broth (cation adjusted) (Becton,

567

Dickinson and Co, Franklin Lakes NJ) using the broth microdilution method according to CLSI

568

guidelines. Inoculum was prepared using the colony resuspension method and plates were

569

incubated with aeration at 37°C for 18 h.

570 571

Protein expression and purification

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cDNA of icrMc from Moraxella catarrhalis strain BC1 (Genbank accession EGE18576)

573

coding for residues 235 to 578 of ICRMc was synthesized by Integrated DNA Technologies and

574

subcloned into the pMCSG53 expression vector that codes for a N-terminal His6-tag and a TEV

575

protease cleavage site. icrMc was expressed in E. coli BL21(DE3) Gold cells, grown to an OD600

576

of 0.6 at 37 °C, chilled to 16 °C and induced overnight with 500 µM isopropyl β-D-

577

thiogalactopyranoside.

578

resuspended in binding buffer [50 mM Hepes (pH 7.5), 100-300 mM sodium chloride, 10 mM

579

imidazole and 2% glycerol (v/v)], lysed by sonication, and cell debris removed via centrifugation

580

at 30,000 x g. Cleared lysate was loaded onto a 5-mL Ni-NTA column (QIAGEN) pre-

Cells were harvested via centrifugation at 5000 x g and pellets

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ACS Chemical Biology

581

equilibrated with binding buffer, extensively washed with binding buffer containing 30 mM

582

imidazole, and protein was eluted using the above buffer with 250 mM imidazole. Fractions

583

containing ICRMc were identified by SDS-polyacrylamide gel electrophoresis and further purified

584

via gel filtration on a HiLoad 16/60 Superdex75 prep-grade column [10 mM Hepes (pH 7.5) and

585

50 mM potassium chloride].

586 587

Crystallization and structure determination

588

All crystallization was performed at room temperature using the sitting drop method and 2 µL

589

protein or protein:ligand mixture plus 2 µL reservoir solution. Zn2+-free ICRMc was crystallized

590

with reservoir solution 0.1 M sodium acetate pH 4.6 and 1.2 M ammonium sulfate and the

591

crystal was cryoprotected in 8% glycerol, 8% ethylene glycol and 8% sucrose. Crystals of Zn2+-

592

bound mono-Zn2+•ICRMc were obtained by soaking apo crystals with 2.5 mM zinc chloride for

593

30 minutes followed by cryoprotection in the above cryosolution.

594

ICRMccatThr315Ala•mono-Zn2+•PetN were obtained from reservoir solution 0.1 M MES pH 6, 22%

595

(w/v) PEG 400, 2.5 mM zinc chloride and 5 mM PetN and the crystal was cryoprotected in

596

paratone oil. Crystals of ICRMccatThr315Ala•di-Zn2+•PEG were obtained from reservoir solution

597

0.1 M Tris pH 8, 28% (w/v) PEG 4k, 3 mM zinc chloride and 2 mM lipid A head-group

598

(Glycobiotech GmbH) and the crystal was cryoprotected in paratone oil. All X-ray diffraction

599

data at 100 K were collected at the Advanced Photon Source, Argonne National Laboratory, Life

600

Sciences Collaborative Access Team beamline 21-ID-D at the following wavelengths

601

corresponding to the measured zinc absorption peak: ICRMc•PO4 – 1.27424 Å / 9730 keV;

602

ICRMc•mono-Zn2+ – 1.27424 Å / 9730 keV; ICRMccatThr315Ala•mono-Zn2+•PEtN – 1.27687 Å /

603

9710 keV; ICRMccatThr315Ala•di-Zn2+•PEG - 1.27815 Å / 9700 keV. X-ray data were reduced with

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Crystals of

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Page 34 of 35

604

XDS 37 and CCP4 Aimless 38 or HKL-3000 39 for the di-Zn2+•PEG structure. The WT structures

605

were solved by Molecular Replacement using the ICRMc sequence-substituted structure of

606

Neisseria meningitis EptA/LptA (PDB id 4kay

607

ICRMccatThr315Ala structures were phased using the anomalous signal from Zn2. Refinement was

608

completed with Phenix.refine and Coot41. All B-factors were refined as isotropic with TLS

609

parameterization. Zn2+, sulfate ions and the positions of the six cysteine residues implicated in

610

disulfide bond formation were verified by the presence of peaks in an anomalous difference map.

611

In the WT ICRMc structure, the peak in the anomalous difference electron density peak was 32 σ /

612

0.148 e-/A3. In the ICRMccatThr315Ala•di-Zn2+ structure, the anomalous difference density peak

613

heights were 91 σ/0.896 e-/A3 and 82 σ/0.827 e-/A3 in one active site, 85 σ/0.839 e-/A3 and 84

614

σ/0.828 e-/A3 in the second active site. In the ICRMccatThr315Ala•mono-Zn2+•PEtN complex, the

615

anomalous different density peak heights were 95.0σ/0.96 e-/A3 and 81.6σ/0.86 e-/A3 in one

616

active site and 85.3 σ/0.90 e-/A3 and 84.3 σ/0.89 e-/A3 in the second active site. All geometry

617

was verified using the Phenix and the wwPDB server.

26

) using Phenix.phaser

40

while the

618 619

Sequence and structural analysis

620

Sequence orthologs of ICRMc, MCR-1, MCR-2, MCR-3, MCR-4, EptA, EptB and EptC were

621

identified in Genbank using BLAST. Sequence alignment was performed using Jalview

622

verified by eye and inspection of structural features of ICRMc.

623

produced by ESPript43. Phylogenetic reconstruction was conducted using the aligned full-length

624

PEtN transferase sequences and the program Mr. Bayes44. Structure similarity searches were

625

performed using the Dali server

626

Model of full-length ICRMc onto EptA was constructing using Phyre2

45

42

and

Sequence alignment was

. Active site volume was calculated by the CastP server

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46

.

. Dimerization interface

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ACS Chemical Biology

627

burial in the ICRMccatThr315Ala crystal structure was calculated using the PDBePISA server 48 and

628

experimentally tested in solution using a Superdex S200 size exclusion column.

629 630

Supporting information

631

The Supporting Information is available free of charge at the ACS Publications website.

632

Sequence alignment of PEtN transferases, size exclusion chromatography of ICRMc,

633

structure of the active site of the dimeric ICRMccatThr315Ala•di-Zn2+•PEG complex, and

634

comparison of the structures of ICRMc with EptA and EptC (PDF).

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