6SUT | pdb_00006sut

Crystal structure of phosphothreonine MCR-2

• PDB DOI: https://doi.org/10.2210/pdb6SUT/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-16 Released: 2020-06-03 
• Deposition Author(s): Hinchliffe, P., Spencer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Resistance to the "last resort" antibiotic colistin: a single-zinc mechanism for phosphointermediate formation in MCR enzymes.

Lythell, E., Suardiaz, R., Hinchliffe, P., Hanpaibool, C., Visitsatthawong, S., Oliveira, A.S.F., Lang, E.J.M., Surawatanawong, P., Lee, V.S., Rungrotmongkol, T., Fey, N., Spencer, J., Mulholland, A.J.

(2020) Chem Commun (Camb) 56: 6874-6877

• PubMed: 32432618 
• DOI: https://doi.org/10.1039/d0cc02520h
• Primary Citation Related Structures: 
  6SUT


• PubMed Abstract: 
  

  MCR (mobile colistin resistance) enzymes catalyse phosphoethanolamine (PEA) addition to bacterial lipid A, threatening the "last-resort" antibiotic colistin. Molecular dynamics and density functional theory simulations indicate that monozinc MCR supports PEA transfer to the Thr285 acceptor, positioning MCR as a mono- rather than multinuclear member of the alkaline phosphatase superfamily.

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Organizational Affiliation: 
• Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. [e-mail] and School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD, UK. [e-mail].
Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. [e-mail] and School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK and Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK and Department of Physical Chemistry, Faculty of Chemistry, Complutense University of Madrid, 28040 Madrid, Spain.
School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD, UK. [e-mail].
Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. [e-mail] and School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK.
Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. [e-mail].
Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand and Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.67 kDa 
• Atom Count: 3,060 
• Modeled Residue Count: 324 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative integral membrane protein	A	324	Escherichia coli	Mutation(s): 0  Gene Names: mcr-2 EC: 2.7.8.43
UniProt
Find proteins for A0A1C3NEV1 (Escherichia coli) Explore A0A1C3NEV1  Go to UniProtKB:  A0A1C3NEV1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR	G [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.08	α = 90
b = 53.57	β = 90
c = 122.669	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Hinchliffe, P., Spencer, J.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2020-07-01
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary