1PNV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report



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 U S A 100: 9238

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

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCOSYLTRANSFERASE GTFAAB404Amycolatopsis orientalisMutation(s): 0 
Gene Names: gtfA
EC: 2.4.1.311
Find proteins for P96558 (Amycolatopsis orientalis)
Explore P96558 
Go to UniProtKB:  P96558
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VANCOMYCINC7Amycolatopsis orientalisMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
vancosamine-(1-2)-beta-D-glucopyranose
D
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYD
Query on TYD

Download Ideal Coordinates CCD File 
A
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OMY
Query on OMY
CL-PEPTIDE LINKINGC9 H10 Cl N O4TYR
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000204
Query on PRD_000204
CVANCOMYCINGlycopeptide /  Antibiotic

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Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000204
Query on PRD_000204
DVANCOMYCINGlycopeptide /  Antibiotic

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.17α = 90
b = 153.17β = 90
c = 100.64γ = 120
Software Package:
Software NamePurpose
SOLVEphasing
RESOLVEmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-12
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary