4R84

Crystal structure of Sialyltransferase from Photobacterium damsela with CMP-3F(a)Neu5Ac bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of sialyltransferase from Photobacterium damselae.

Huynh, N.Li, Y.Yu, H.Huang, S.Lau, K.Chen, X.Fisher, A.J.

(2014) FEBS Lett 588: 4720-4729

  • DOI: https://doi.org/10.1016/j.febslet.2014.11.003
  • Primary Citation of Related Structures:  
    4R83, 4R84, 4R9V

  • PubMed Abstract: 

    Sialyltransferase structures fall into either GT-A or GT-B glycosyltransferase fold. Some sialyltransferases from the Photobacterium genus have been shown to contain an additional N-terminal immunoglobulin (Ig)-like domain. Photobacterium damselae α2-6-sialyltransferase has been used efficiently in enzymatic and chemoenzymatic synthesis of α2-6-linked sialosides. Here we report three crystal structures of this enzyme. Two structures with and without a donor substrate analog CMP-3F(a)Neu5Ac contain an immunoglobulin (Ig)-like domain and adopt the GT-B sialyltransferase fold. The binary structure reveals a non-productive pre-Michaelis complex, which are caused by crystal lattice contacts that prevent the large conformational changes. The third structure lacks the Ig-domain. Comparison of the three structures reveals small inherent flexibility between the two Rossmann-like domains of the GT-B fold.


  • Organizational Affiliation

    Cell Biology Graduate Program, University of California, One Shields Avenue, Davis, CA 95616, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sialyltransferase 0160
A, B, C, D
503Photobacterium damselaeMutation(s): 0 
Gene Names: bst
EC: 2.4.99.1
UniProt
Find proteins for O66375 (Photobacterium damselae)
Explore O66375 
Go to UniProtKB:  O66375
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66375
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.34α = 99.02
b = 81.45β = 91.59
c = 111.21γ = 101.2
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2015-01-14
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description