2HLH

Crystal structure of fucosyltransferase NodZ from Bradyrhizobium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High-resolution structure of NodZ fucosyltransferase involved in the biosynthesis of the nodulation factor.

Brzezinski, K.Stepkowski, T.Panjikar, S.Bujacz, G.Jaskolski, M.

(2007) Acta Biochim Pol 54: 537-549

  • Primary Citation of Related Structures:  
    2HHC, 2HLH, 2OCX

  • PubMed Abstract: 

    The fucosyltransferase NodZ is involved in the biosynthesis of the nodulation factor in nitrogen-fixing symbiotic bacteria. It catalyzes alpha1,6 transfer of l-fucose from GDP-fucose to the reducing residue of the synthesized Nod oligosaccharide. We present the structure of the NodZ protein from Bradyrhizobium expressed in Escherichia coli and crystallized in the presence of phosphate ions in two crystal forms. The enzyme is arranged into two domains of nearly equal size. Although NodZ falls in one broad class (GT-B) with other two-domain glycosyltransferases, the topology of its domains deviates from the canonical Rossmann fold, with particularly high distortions in the N-terminal domain. Mutational data combined with structural and sequence alignments indicate residues of potential importance in GDP-fucose binding or in the catalytic mechanism. They are all clustered in three conserved sequence motifs located in the C-terminal domain.


  • Organizational Affiliation

    Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznań, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nodulation fucosyltransferase330Bradyrhizobium sp. WM9Mutation(s): 0 
Gene Names: nodZ
EC: 2.4.1
UniProt
Find proteins for Q9AQ17 (Bradyrhizobium sp. (strain WM9))
Explore Q9AQ17 
Go to UniProtKB:  Q9AQ17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AQ17
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.1α = 90
b = 130.1β = 90
c = 83.3γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-17
    Type: Initial release
  • Version 1.1: 2008-02-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description