7nhe

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==Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex==
==Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex==
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<StructureSection load='7nhe' size='340' side='right'caption='[[7nhe]]' scene=''>
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<StructureSection load='7nhe' size='340' side='right'caption='[[7nhe]], [[Resolution|resolution]] 2.23&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NHE FirstGlance]. <br>
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<table><tr><td colspan='2'>[[7nhe]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NHE FirstGlance]. <br>
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</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=7nhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nhe OCA], [https://pdbe.org/7nhe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nhe RCSB], [https://www.ebi.ac.uk/pdbsum/7nhe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nhe ProSAT]</span></td></tr>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KPR:[(~{E},4~{S})-4-AZANYL-3-OXIDANYLIDENE-PENT-1-ENYL]+DIHYDROGEN+PHOSPHATE'>KPR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyridoxal_5'-phosphate_synthase_(glutamine_hydrolyzing) Pyridoxal 5'-phosphate synthase (glutamine hydrolyzing)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.6 4.3.3.6] </span></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=7nhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nhe OCA], [https://pdbe.org/7nhe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nhe RCSB], [https://www.ebi.ac.uk/pdbsum/7nhe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nhe ProSAT]</span></td></tr>
</table>
</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/PDX13_ARATH PDX13_ARATH]] Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by PDX2. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively. Also plays an indirect role in resistance to singlet oxygen-generating photosensitizers.<ref>PMID:16157873</ref> <ref>PMID:16236150</ref> <ref>PMID:17468224</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The Pdx1 enzyme catalyses condensation of two carbohydrates and ammonia to form pyridoxal 5-phosphate (PLP) via an imine relay mechanism of carbonyl intermediates. The I333 intermediate characterised here using structural, UV-vis absorption spectroscopy and mass spectrometry analyses rationalises stereoselective deprotonation and subsequent substrate assisted phosphate elimination, central to PLP biosynthesis.
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Trapping and structural characterisation of a covalent intermediate in vitamin B6 biosynthesis catalysed by the Pdx1 PLP synthase.,Rodrigues MJ, Giri N, Royant A, Zhang Y, Bolton R, Evans G, Ealick SE, Begley T, Tews I RSC Chem Biol. 2021 Oct 25;3(2):227-230. doi: 10.1039/d1cb00160d. eCollection, 2022 Feb 9. PMID:35360887<ref>PMID:35360887</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 7nhe" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Begley T]]
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[[Category: Begley, T]]
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[[Category: Bolton R]]
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[[Category: Bolton, R]]
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[[Category: Ealick SE]]
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[[Category: Ealick, S E]]
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[[Category: Evans G]]
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[[Category: Evans, G]]
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[[Category: Giri N]]
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[[Category: Giri, N]]
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[[Category: Rodrigues MJ]]
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[[Category: Rodrigues, M J]]
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[[Category: Royant A]]
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[[Category: Royant, A]]
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[[Category: Tews I]]
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[[Category: Tews, I]]
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[[Category: Zhang Y]]
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[[Category: Zhang, Y]]
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[[Category: Lyase]]
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[[Category: Pdx1]]
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[[Category: Plp synthase]]
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[[Category: Vitamin b6 biosythesis]]

Revision as of 10:19, 13 April 2022

Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex

PDB ID 7nhe

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