Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

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

Macromolecule Content

• Total Structure Weight: 31.89 kDa 
• Atom Count: 1938 
• Modelled Residue Count: 227 
• Deposited Residue Count: 263 
• Unique protein chains: 1

3VMR

Crystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with moenomycin

• PDB DOI: 10.2210/pdb3VMR/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2011-12-15 Released: 2012-04-18 
• Deposition Author(s): Huang, C.Y., Shih, H.W., Lin, L.Y., Tien, Y.W., Cheng, T.J.R., Cheng, W.C., Wong, C.H., Ma, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.69 Å
• R-Value Free: 0.309 
• R-Value Work: 0.303 
• R-Value Observed: 0.304 

Literature

Crystal structure of Staphylococcus aureus transglycosylase in complex with a lipid II analog and elucidation of peptidoglycan synthesis mechanism

Huang, C.Y., Shih, H.W., Lin, L.Y., Tien, Y.W., Cheng, T.J.R., Cheng, W.C., Wong, C.H., Ma, C.

(2012) Proc Natl Acad Sci U S A 109: 6496-6501

• PubMed: 22493270 
• DOI: 10.1073/pnas.1203900109
• Primary Citation of Related Structures:  
  3VMQ, 3VMR, 3VMS, 3VMT


• PubMed Abstract: 
  

Bacterial transpeptidase and transglycosylase on the surface are essential for cell wall synthesis, and many antibiotics have been developed to target the transpeptidase; however, the problem of antibiotic resistance has arisen and caused a major threat in bacterial infection. The transglycosylase has been considered to be another excellent target, but no antibiotics have been developed to target this enzyme. Here, we determined the crystal structure of the Staphylococcus aureus membrane-bound transglycosylase, monofunctional glycosyltransferase, in complex with a lipid II analog to 2.3 Å resolution. Our results showed that the lipid II-contacting residues are not only conserved in WT and drug-resistant bacteria but also significant in enzymatic activity. Mechanistically, we proposed that K140 and R148 in the donor site, instead of the previously proposed E156, are used to stabilize the pyrophosphate-leaving group of lipid II, and E100 in the acceptor site acts as general base for the 4-OH of GlcNAc to facilitate the transglycosylation reaction. This mechanism, further supported by mutagenesis study and the structure of monofunctional glycosyltransferase in complex with moenomycin in the donor site, provides a direction for antibacterial drugs design.

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Organizational Affiliation: 

Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monofunctional glycosyltransferase	A	263	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: mgt, SAV1874 EC: 2.4 (PDB Primary Data), 2.4.1.129 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q99T05 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q99T05  Go to UniProtKB:  Q99T05

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M0E	B [auth A]	MOENOMYCIN C69 H106 N5 O34 P NXPRJQIAIORCGO-ZLPAOQQDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.69 Å
• R-Value Free: 0.309 
• R-Value Work: 0.303 
• R-Value Observed: 0.304 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.423	α = 90
b = 52.852	β = 90
c = 54.585	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-15 
• Released Date: 2012-04-18 
Deposition Author(s): Huang, C.Y., Shih, H.W., Lin, L.Y., Tien, Y.W., Cheng, T.J.R., Cheng, W.C., Wong, C.H., Ma, C.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references