2OCX

Crystal structure of Se-Met fucosyltransferase NodZ from Bradyrhizobium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 ...

    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.


    Related Citations: 
    • Bacterial nodulation protein NodZ is a chitin oligosaccharide fucosyltransferase which can also recognize related substrates of animal origin
      Quinto, C.,Wijfjes, A.H.,Bloemberg, G.V.,Blok-Tip, L.,Lopez-Lara, I.M.,Lugtenberg, B.J.,Thomas-Oates, J.E.,Spaink, H.P.
      (1997) Proc.Natl.Acad.Sci.USA 94: 4336
    • Cloning, purification, crystallization and preliminary crystallographic studies of Bradyrhizobium fucosyltransferase NodZ
      Brzezinski, K.,Rogozinski, B.,Stepkowski, T.,Bujacz, G.,Jaskolski, M.
      (2004) Acta Crystallogr.,Sect.D 60: 344
    • Rhizobium sp. strain NGR234 NodZ protein is a fucosyltransferase
      Quesada-Vincens, D.,Fellay, R.,Nasim, T.,Viprey, V.,Burger, U.,Prome, J.C.,Broughton, W.J.,Jabbouri, S.
      (1997) J.Bacteriol. 179: 5087


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nodulation fucosyltransferase NodZ
A
330Bradyrhizobium sp. (strain WM9)Mutation(s): 0 
Gene Names: nodZ
EC: 2.4.1.-
Find proteins for Q9AQ17 (Bradyrhizobium sp. (strain WM9))
Go to UniProtKB:  Q9AQ17
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 124.200α = 90.00
b = 124.200β = 90.00
c = 96.200γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
DENZOdata reduction
Auto-Rickshawphasing
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-18
    Type: Advisory, Refinement description