Crystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with a Lipid II analog

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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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

  • DOI: https://doi.org/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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Monofunctional glycosyltransferase
A, B
263Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: mgtSAV1874
EC: 2.4 (PDB Primary Data), (UniProt)
Membrane Entity: Yes 
Find proteins for Q99T05 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore Q99T05 
Go to UniProtKB:  Q99T05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99T05
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LHI

Download Ideal Coordinates CCD File 
C [auth A][(2R,3R,4R,5S,6R)-4-[(2R)-1-[[(2S)-1-[2-[2-[2-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]ethoxy]ethoxy]ethylamino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]oxy-3-acetamido-5-[(2S,3R,4R,5R,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-(hydroxymethyl)oxan-2-yl] [oxidanyl(3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenoxy)phosphoryl] hydrogen phosphate
C93 H155 N7 O23 P2 S
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.493α = 90
b = 67.429β = 90
c = 152.186γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description