1QGS

UDP-MAGNESIUM COMPLEX OF SPSA FROM BACILLUS SUBTILIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms.

Charnock, S.J.Davies, G.J.

(1999) Biochemistry 38: 6380-6385

  • DOI: https://doi.org/10.1021/bi990270y
  • Primary Citation of Related Structures:  
    1QG8, 1QGQ, 1QGS

  • PubMed Abstract: 

    The enzymatic formation of glycosidic bonds may be catalyzed by the transfer of the glycosyl moiety from an activated nucleotide-diphospho-sugar donor to a specific acceptor. SpsA is a glycosyltransferase implicated in the synthesis of the spore coat of Bacillus subtilis, whose homologues include cellulose synthase and many lipopolysaccharide and bacterial O-antigen synthases. The three-dimensional crystal structure of SpsA has been determined by conventional MIR techniques at a resolution of 1.5 A. It is a two-domain protein with a nucleotide-binding domain together with an acceptor binding domain which features a disordered loop spanning the active site. The structures of SpsA in complex with both Mg-UDP and Mn-UDP have also been determined at 2.0 and 1.7 A, respectively. These complexes, together with the sequence conservation, begin to shed light on the mechanism of this ubiquitous family of inverting glycosyltransferases.


  • Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA)255Bacillus subtilisMutation(s): 0 
Gene Names: SPSA
UniProt
Find proteins for P39621 (Bacillus subtilis (strain 168))
Explore P39621 
Go to UniProtKB:  P39621
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39621
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.42α = 90
b = 141.997β = 90
c = 81.439γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-04
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary