3SIW

Crystal structure of NodZ alpha-1,6-fucosyltransferase co-crystallized with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of NodZ alpha-1,6-fucosyltransferase in complex with GDP and GDP-fucose

Brzezinski, K.Dauter, Z.Jaskolski, M.

(2012) Acta Crystallogr.,Sect.D 68: 160-168

  • DOI: 10.1107/S0907444911053157
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rhizobial NodZ α1,6-fucosyltransferase (α1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5'-diphosphate-β-L-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key sign ...

    Rhizobial NodZ α1,6-fucosyltransferase (α1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5'-diphosphate-β-L-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key signalling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. To date, only two α1,6-FucT structures have been determined, both without any donor or acceptor molecule that could highlight the structural background of the catalytic mechanism. Here, the first crystal structures of α1,6-FucT in complex with its substrate GDP-Fuc and with GDP, which is a byproduct of the enzymatic reaction, are presented. The crystal of the complex with GDP-Fuc was obtained through soaking of native NodZ crystals with the ligand and its structure has been determined at 2.35 Å resolution. The fucose residue is exposed to solvent and is disordered. The enzyme-product complex crystal was obtained by cocrystallization with GDP and an acceptor molecule, penta-N-acetyl-L-glucosamine (penta-NAG). The structure has been determined at 1.98 Å resolution, showing that only the GDP molecule is present in the complex. In both structures the ligands are located in a cleft formed between the two domains of NodZ and extend towards the C-terminal domain, but their conformations differ significantly. The structures revealed that residues in three regions of the C-terminal domain, which are conserved among α1,2-, α1,6- and protein O-fucosyltransferases, are involved in interactions with the sugar-donor molecule. There is also an interaction with the side chain of Tyr45 in the N-terminal domain, which is very unusual for a GT-B-type glycosyltransferase. Only minor conformational changes of the protein backbone are observed upon ligand binding. The only exception is a movement of the loop located between strand βC2 and helix αC3. In addition, there is a shift of the αC3 helix itself upon GDP-Fuc binding.


    Related Citations: 
    • 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
    • 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
    • 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
    • Crystal structure of human alpha 1,6-fucosyltransferase, FUT8
      Ihara, H.,Ikeda, Y.,Toma, S.,Wang, X.,Suzuki, T.,Gu, J.,Miyoshi, E.,Tsukihara, T.,Honke, K.,Matsumoto, A.,Nakagawa, A.,Taniguchi, N.
      (2007) Glycobiology 17: 455
    • Structure and Mechanism of Helicobacter pylori Fucosyltransferase: A basis for lipopolysaccharide variation and inhibitor design
      Sun, H.Y.,Lin, S.W.,Ko, T.P.,Liu, C.L.,Wang, H.J.,Lin, C.H.
      (2007) J.Biol.Chem. 282: 9973
    • 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

    Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.




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
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 123.900α = 90.00
b = 123.900β = 90.00
c = 95.200γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-3000data reduction
PHASERphasing
SERGUIdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Database references, Refinement description