1H7Q

dTDP-MANGANESE COMPLEX OF SPSA FROM BACILLUS SUBTILIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-Dimensional Structures of the Mn and Mg Dtdp Complexes of the Family Gt-2 Glycosyltransferase Spsa: A Comparison with Related Ndp-Sugar Glycosyltransferases.

Tarbouriech, N.Charnock, S.J.Davies, G.J.

(2001) J.Mol.Biol. 314: 655

  • DOI: 10.1006/jmbi.2001.5159
  • Primary Citation of Related Structures:  1H7L

  • PubMed Abstract: 
  • The vast majority of glycosidic-bond synthesis in nature is performed by glycosyltransferases, which use activated glycosides as the sugar donor. Typically, the activated leaving group is a nucleoside phosphate, lipid phosphate or phosphate. The nucl ...

    The vast majority of glycosidic-bond synthesis in nature is performed by glycosyltransferases, which use activated glycosides as the sugar donor. Typically, the activated leaving group is a nucleoside phosphate, lipid phosphate or phosphate. The nucleotide-sugar-dependent glycosyltransferases fall into over 50 sequence-based families, with the largest and most widespread family of inverting transferases named family GT-2. Here, we present the three-dimensional crystal structure of SpsA, the first and currently the only structural representative from family GT-2, in complex with both Mn-dTDP and Mg-dTDP at a resolution of 2 A. These structures reveal how SpsA and related enzymes may display nucleotide plasticity and permit a comparison of the catalytic centre of this enzyme with those from related sequence families whose three-dimensional structures have recently been determined. Family GT-2 enzymes, together with enzymes from families 7, 13 and 43, appear to form a clan of related structures with identical catalytic apparatus and reaction mechanism.


    Organizational Affiliation

    Department of Chemistry, Structural Biology Laboratory, Heslington, Y010 5DD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA
A
255Bacillus subtilis (strain 168)Gene Names: spsA
Find proteins for P39621 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39621
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-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
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 47.372α = 90.00
b = 142.060β = 90.00
c = 81.425γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance