1RRV

X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

Crystal Structure of Vancosaminyltransferase Gtfd from the Vancomycin Biosynthetic Pathway: Interactions with Acceptor and Nucleotide Ligands

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

(2004) Biochemistry 43: 5170

  • DOI: 10.1021/bi036130c

  • PubMed Abstract: 
  • The TDP-vancosaminyltransferase GtfD catalyzes the attachment of L-vancosamine to a monoglucosylated heptapeptide intermediate during the final stage of vancomycin biosynthesis. Glycosyltransferases from this and similar antibiotic pathways are poten ...

    The TDP-vancosaminyltransferase GtfD catalyzes the attachment of L-vancosamine to a monoglucosylated heptapeptide intermediate during the final stage of vancomycin biosynthesis. Glycosyltransferases from this and similar antibiotic pathways are potential tools for the design of new compounds that are effective against vancomycin resistant bacterial strains. We have determined the X-ray crystal structure of GtfD as a complex with TDP and the natural glycopeptide substrate at 2.0 A resolution. GtfD, a member of the bidomain GT-B glycosyltransferase superfamily, binds TDP in the interdomain cleft, while the aglycone acceptor binds in a deep crevice in the N-terminal domain. However, the two domains are more interdependent in terms of substrate binding and overall structure than was evident in the structures of closely related glycosyltransferases GtfA and GtfB. Structural and kinetic analyses support the identification of Asp13 as a catalytic general base, with a possible secondary role for Thr10. Several residues have also been identified as being involved in donor sugar binding and recognition.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOSYLTRANSFERASE GTFD
A, B
416Amycolatopsis orientalisMutation(s): 0 
Gene Names: gtfD
EC: 2.4.1.322
Find proteins for Q9AFC7 (Amycolatopsis orientalis)
Go to UniProtKB:  Q9AFC7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DESVANCOSAMINYL VANCOMYCIN
C, D
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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

Download SDF File 
Download CCD File 
A, B
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000205
Query on PRD_000205
C,DDESVANCOSAMINYL VANCOMYCINGlycopeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.670α = 90.00
b = 64.120β = 91.73
c = 144.080γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
CNSrefinement
AMoREphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-18
    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
  • Version 1.5: 2017-10-11
    Type: Refinement description
  • Version 1.6: 2017-11-01
    Type: Derived calculations