3six | pdb_00003six

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

spinqualitylabelsall models 3six, resolution 2.35Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3six is a 1 chain structure with sequence from Bradyrhizobium sp.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CL, GDP, PO4 Related: 2ocx, 2hhc, 2hlh, 2nzw, 2nzx, 2nzy, 2de0, 3siw Gene: nodZ (Bradyrhizobium sp.) Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed Rhizobial NodZ alpha1,6-fucosyltransferase (alpha1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5'-diphosphate-beta-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 alpha1,6-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 alpha1,6-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 A 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 A 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 alpha1,2-, alpha1,6- 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 betaC2 and helix alphaC3. In addition, there is a shift of the alphaC3 helix itself upon GDP-Fuc binding. Structures of NodZ alpha1,6-fucosyltransferase in complex with GDP and GDP-fucose.,Brzezinski K, Dauter Z, Jaskolski M Acta Crystallogr D Biol Crystallogr. 2012 Feb;68(Pt 2):160-8. Epub 2012 Jan 6. PMID:22281745 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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