1PNV

Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and Vancomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of the Tdp-Epi-Vancosaminyltransferase Gtfa from the Chloroeremomycin Biosynthetic Pathway.

Mulichak, A.M.Losey, H.C.Lu, W.Wawrzak, Z.Walsh, C.T.Garavito, R.M.

(2003) Proc.Natl.Acad.Sci.USA 100: 9238

  • DOI: 10.1073/pnas.1233577100
  • Primary Citation of Related Structures:  1PN3

  • PubMed Abstract: 
  • During the biosynthesis of the vancomycin-class antibiotic chloroeremomycin, TDP-epi-vancosaminyltransferase GtfA catalyzes the attachment of 4-epi-vancosamine from a TDP donor to the beta-OHTyr-6 of the aglycone cosubstrate. Glycosyltransferases fro ...

    During the biosynthesis of the vancomycin-class antibiotic chloroeremomycin, TDP-epi-vancosaminyltransferase GtfA catalyzes the attachment of 4-epi-vancosamine from a TDP donor to the beta-OHTyr-6 of the aglycone cosubstrate. Glycosyltransferases from this pathway are potential tools for the combinatorial design of new antibiotics that are effective against vancomycin-resistant bacterial strains. These enzymes are members of the GT-B glycosyltransferase superfamily, which share a homologous bidomain topology. We present the 2.8-A crystal structures of GtfA complexes with vancomycin and the natural monoglycosylated peptide substrate, representing the first direct observation of acceptor substrate binding among closely related glycosyltransferases. The acceptor substrates bind to the N-terminal domain such that the aglycone substrate's reactive hydroxyl group hydrogen bonds to the side chains of Ser-10 and Asp-13, thus identifying these as residues of potential catalytic importance. As well as an open form of the enzyme, the crystal structures have revealed a closed form in which a TDP ligand is bound at a donor substrate site in the interdomain cleft, thereby illustrating not only binding interactions, but the conformational changes in the enzyme that accompany substrate binding.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOSYLTRANSFERASE GTFA
A, B
404Amycolatopsis orientalisGene Names: gtfA
EC: 2.4.1.311
Find proteins for P96558 (Amycolatopsis orientalis)
Go to UniProtKB:  P96558
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VANCOMYCIN
C
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
C
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
TYD
Query on TYD

Download SDF File 
Download CCD File 
A
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
RER
Query on RER

Download SDF File 
Download CCD File 
C
(1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose
VANCOSAMINE
C7 H15 N O3
OIJZDPGKNVKVBL-WNJXEPBRSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000204
Query on PRD_000204
CVANCOMYCINGlycopeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.170α = 90.00
b = 153.170β = 90.00
c = 100.640γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
DENZOdata reduction
RESOLVEmodel building
RESOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-12
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other