3SIX

Crystal structure of NodZ alpha-1,6-fucosyltransferase soaked with GDP-fucose

Summary for 3SIX

• Entry DOI: 10.2210/pdb3six/pdb
• Related: 2DE0 2HHC 2HLH 2NZW 2NZX 2NZY 2OCX 3SIW
• Descriptor: Nodulation fucosyltransferase NodZ, GUANOSINE-5'-DIPHOSPHATE, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: family gt23 glycosyltransferase, gt-b fold, alfa1, 6-fucosyltransferase, nodulation protein, chitooligosaccharide fucosylation, nod factor biosynthesis, nitrogen fixation, legume-rhizobium symbiosis, transferase
• Biological source: Bradyrhizobium sp.
• Total number of polymer chains: 1
• Total formula weight: 38402.61

Authors

Brzezinski, K.,Dauter, Z.,Jaskolski, M. (deposition date: 2011-06-20, release date: 2012-02-08, Last modification date: 2023-09-13)

Primary citation

Brzezinski, K.,Dauter, Z.,Jaskolski, M.
Structures of NodZ alpha-1,6-fucosyltransferase in complex with GDP and GDP-fucose
Acta Crystallogr.,Sect.D, 68:160-168, 2012

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 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.

PubMed: 22281745
DOI: 10.1107/S0907444911053157

Experimental method

X-RAY DIFFRACTION (2.35 Å)