5M2H | pdb_00005m2h

Crystal structure of vancomycin-Zn(II)-citrate complex

• PDB DOI: https://doi.org/10.2210/pdb5M2H/pdb

• Classification: ANTIBIOTIC
• Organism(s): Amycolatopsis orientalis
• Mutation(s): No 


• Deposited: 2016-10-13 Released: 2017-07-19 
• Deposition Author(s): Zarkan, A., Macklyne, H.-R., Chirgadze, D.Y., Bond, A.D., Hesketh, A.R., Hong, H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.118 (Depositor), 0.126 (DCC) 
• R-Value Work: 
  0.105 (Depositor), 0.112 (DCC) 
• R-Value Observed: 
  0.106 (Depositor) 

Literature

Zn(II) mediates vancomycin polymerization and potentiates its antibiotic activity against resistant bacteria.

Zarkan, A., Macklyne, H.R., Chirgadze, D.Y., Bond, A.D., Hesketh, A.R., Hong, H.J.

(2017) Sci Rep 7: 4893-4893

• PubMed: 28687742 
• DOI: https://doi.org/10.1038/s41598-017-04868-2
• Primary Citation Related Structures: 
  5M2H, 5M2K


• PubMed Abstract: 
  

  Vancomycin is known to bind to Zn(II) and can induce a zinc starvation response in bacteria. Here we identify a novel polymerization of vancomycin dimers by structural analysis of vancomycin-Zn(II) crystals and fibre X-ray diffraction. Bioassays indicate that this structure is associated with an increased antibiotic activity against bacterial strains possessing high level vancomycin resistance mediated by the reprogramming of peptidoglycan biosynthesis to use precursors terminating in D-Ala-D-Lac in place of D-Ala-D-Ala. Polymerization occurs via interaction of Zn(II) with the N-terminal methylleucine group of vancomycin, and we show that the activity of other glycopeptide antibiotics with this feature can also be similarly augmented by Zn(II). Construction and analysis of a model strain predominantly using D-Ala-D-Lac precursors for peptidoglycan biosynthesis during normal growth supports the hypothesis that Zn(II) mediated vancomycin polymerization enhances the binding affinity towards these precursors.

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Organizational Affiliation: 
• Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
Cambridge Systems Biology Centre, University of Cambridge, Cambridge, CB2 1QW, UK.
Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK. [e-mail].
Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK. [e-mail].

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 3.68 kDa 
• Atom Count: 320 
• Modeled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vancomycin	A, B	7	Amycolatopsis orientalis	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
vancosamine-(1-2)-beta-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G14263HU GlyCosmos: G14263HU

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	H [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
CIT	F [auth A], G [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3FG	A, B	L-PEPTIDE LINKING	C8 H9 N O4		--
GHP	A, B	D-PEPTIDE LINKING	C8 H9 N O3		--
MLU	A, B	D-PEPTIDE LINKING	C7 H15 N O2		--
OMY	A, B	L-PEPTIDE LINKING	C9 H10 Cl N O4		TYR
OMZ	A, B	D-PEPTIDE LINKING	C9 H10 Cl N O4		--

Biologically Interesting Molecules (External Reference) 

2 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000204	A, B	Vancomycin	Glycopeptide / Antibiotic

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000204	C, D	Vancomycin	Glycopeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.118 (Depositor), 0.126 (DCC) 
• R-Value Work:  0.105 (Depositor), 0.112 (DCC) 
• R-Value Observed: 0.106 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.038	α = 90
b = 57.481	β = 90
c = 21.638	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-19 
Deposition Author(s): Zarkan, A., Macklyne, H.-R., Chirgadze, D.Y., Bond, A.D., Hesketh, A.R., Hong, H.-J.

Revision History  

• Version 1.0: 2017-07-19
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 2.0: 2019-04-24
  Changes: Data collection, Polymer sequence
• Version 2.1: 2019-07-10
  Changes: Data collection
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Structure summary