6BNE | pdb_00006bne

Crystal structure of the intrinsic colistin resistance enzyme ICR(Mc) from Moraxella catarrhalis, catalytic domain, phosphate-bound complex

• PDB DOI: https://doi.org/10.2210/pdb6BNE/pdb

• Classification: TRANSFERASE
• Organism(s): Moraxella sp. HMSC061H09
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-16 Released: 2018-01-31 
• Deposition Author(s): Stogios, P.J., Evdokimova, E., Wawrzak, Z., Di Leo, R., Savchenko, A., Anderson, W.F., Satchell, K.J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.271 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Substrate recognition by a colistin resistance enzyme from Moraxella catarrhalis.

Stogios, P.J., Cox, G., Zubyk, H.L., Evdokimova, E., Wawrzak, Z., Wright, G.D., Savchenko, A.

(2018) ACS Chem Biol 

• PubMed: 29631403 
• DOI: https://doi.org/10.1021/acschembio.8b00116
• Primary Citation Related Structures: 
  6BNC, 6BND, 6BNE, 6BNF


• PubMed Abstract: 
  

  Lipid A phosphoethanolamine (PEtN) transferases render bacteria resistant to the last resort antibiotic colistin. The recent discoveries of pathogenic bacteria harboring plasmid-borne PEtN transferase ( mcr) genes have illustrated the serious potential for wide dissemination of these resistance elements. The origin of mcr-1 is traced to Moraxella species co-occupying environmental niches with Enterobacteriaceae. Here, we describe the crystal structure of the catalytic domain of the chromosomally encoded colistin resistance PEtN transferase, ICR ^Mc (for intrinsic colistin resistance) of Moraxella catarrhalis. The ICR ^Mc structure in complex with PEtN reveals key molecular details including specific residues involved in catalysis and PEtN binding. It also demonstrates that ICR ^Mc catalytic domain dimerization is required for substrate binding. Our structure-guided phylogenetic analysis provides sequence signatures defining potentially colistin-active representatives in this enzyme family. Combined, these results advance the molecular and mechanistic understanding of PEtN transferases and illuminate their origins.

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Organizational Affiliation: 
• Center for Structural Genomics of Infectious Diseases (CSGID).
Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research , McMaster University , Hamilton , Ontario L8S 4K1 , Canada.
LS-CAT, Synchrotron Research Center , Northwestern University , Argonne , Illinois 60439 , United States.
Department of Microbiology, Immunology and Infectious Diseases, Health Research Innovation Centre , University of Calgary , 3330 Hospital Drive NW, HRIC-2C66 , Calgary , Alberta T2N 4N1 , Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.51 kDa 
• Atom Count: 2,748 
• Modeled Residue Count: 336 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoethanolamine transferase	A	344	Moraxella sp. HMSC061H09	Mutation(s): 0  Gene Names: HMPREF2573_04170
UniProt
Find proteins for A0ACD6BA11 (Moraxella sp. HMSC061H09) Explore A0ACD6BA11  Go to UniProtKB:  A0ACD6BA11

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.271 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.524	α = 90
b = 147.524	β = 90
c = 147.524	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Stogios, P.J., Evdokimova, E., Wawrzak, Z., Di Leo, R., Savchenko, A., Anderson, W.F., Satchell, K.J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Author supporting evidence
• Version 1.2: 2018-04-25
  Changes: Data collection, Database references
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary