7nhf: Difference between revisions
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==Crystal structure of Arabidopsis thaliana Pdx1K166R== | ==Crystal structure of Arabidopsis thaliana Pdx1K166R== | ||
<StructureSection load='7nhf' size='340' side='right'caption='[[7nhf]]' scene=''> | <StructureSection load='7nhf' size='340' side='right'caption='[[7nhf]], [[Resolution|resolution]] 2.35Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NHF FirstGlance]. <br> | <table><tr><td colspan='2'>[[7nhf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NHF FirstGlance]. <br> | ||
</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=7nhf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nhf OCA], [https://pdbe.org/7nhf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nhf RCSB], [https://www.ebi.ac.uk/pdbsum/7nhf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nhf ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | ||
<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> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7nhf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nhf OCA], [https://pdbe.org/7nhf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nhf RCSB], [https://www.ebi.ac.uk/pdbsum/7nhf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nhf ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[[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> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7nhf" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Begley T]] | [[Category: Begley, T]] | ||
[[Category: Bolton R]] | [[Category: Bolton, R]] | ||
[[Category: Ealick | [[Category: Ealick, S E]] | ||
[[Category: Evans G]] | [[Category: Evans, G]] | ||
[[Category: Giri N]] | [[Category: Giri, N]] | ||
[[Category: Rodrigues | [[Category: Rodrigues, M J]] | ||
[[Category: Royant A]] | [[Category: Royant, A]] | ||
[[Category: Tews I]] | [[Category: Tews, I]] | ||
[[Category: Zhang Y]] | [[Category: Zhang, Y]] | ||
[[Category: Lyase]] | |||
[[Category: Pdx1]] | |||
[[Category: Plp synthase]] | |||
[[Category: Vitamin b6 biosythesis]] | |||
Revision as of 10:20, 13 April 2022
Crystal structure of Arabidopsis thaliana Pdx1K166R
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