1H7L

dTDP-MAGNESIUM COMPLEX OF SPSA FROM BACILLUS SUBTILIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.228 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.4 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: https://doi.org/10.1006/jmbi.2001.5159
  • Primary Citation of Related Structures:  
    1H7L, 1H7Q

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA255Bacillus subtilisMutation(s): 0 
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: 1.98 Å
  • R-Value Free:  0.228 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.32α = 90
b = 142.31β = 90
c = 81.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TYDClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary