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| | <StructureSection load='3siw' size='340' side='right'caption='[[3siw]], [[Resolution|resolution]] 1.98Å' scene=''> | | <StructureSection load='3siw' size='340' side='right'caption='[[3siw]], [[Resolution|resolution]] 1.98Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3siw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Brasw Brasw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SIW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3siw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_sp._WM9 Bradyrhizobium sp. WM9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SIW FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ocx|2ocx]], [[2hhc|2hhc]], [[2hlh|2hlh]], [[2nzw|2nzw]], [[2nzx|2nzx]], [[2nzy|2nzy]], [[2de0|2de0]], [[3six|3six]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nodZ ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=133505 BRASW])</td></tr>
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| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3siw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3siw OCA], [https://pdbe.org/3siw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3siw RCSB], [https://www.ebi.ac.uk/pdbsum/3siw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3siw ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3siw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3siw OCA], [https://pdbe.org/3siw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3siw RCSB], [https://www.ebi.ac.uk/pdbsum/3siw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3siw ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q9AQ17_BRASW Q9AQ17_BRASW] |
| - | 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.
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| - | | + | |
| - | 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<ref>PMID:22281745</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 3siw" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Brasw]] | + | [[Category: Bradyrhizobium sp. WM9]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Brzezinski, K]] | + | [[Category: Brzezinski K]] |
| - | [[Category: Dauter, Z]] | + | [[Category: Dauter Z]] |
| - | [[Category: Jaskolski, M]] | + | [[Category: Jaskolski M]] |
| - | [[Category: 6-fucosyltransferase]]
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| - | [[Category: Alfa1]]
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| - | [[Category: Chitooligosaccharide fucosylation]]
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| - | [[Category: Family gt23 glycosyltransferase]]
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| - | [[Category: Gt-b fold]]
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| - | [[Category: Legume-rhizobium symbiosis]]
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| - | [[Category: Nitrogen fixation]]
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| - | [[Category: Nod factor biosynthesis]]
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| - | [[Category: Nodulation protein]]
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| - | [[Category: Transferase]]
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