4keq: Difference between revisions
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New page: '''Unreleased structure''' The entry 4keq is ON HOLD Authors: Kobayashi, J., Yoshikane, Y., Baba, S., Mizutani, K., Takahashi, N., Mikami, B., Yagi, T. Description: Crystal structure o... |
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==Crystal structure of 4-pyridoxolactonase, 5-pyridoxolactone bound== | |||
<StructureSection load='4keq' size='340' side='right'caption='[[4keq]], [[Resolution|resolution]] 2.28Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4keq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_japonicum_MAFF_303099 Mesorhizobium japonicum MAFF 303099]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KEQ FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.279Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5PN:7-HYDROXY-6-METHYLFURO[3,4-C]PYRIDIN-3(1H)-ONE'>5PN</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4keq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4keq OCA], [https://pdbe.org/4keq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4keq RCSB], [https://www.ebi.ac.uk/pdbsum/4keq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4keq ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PDLA_RHILO PDLA_RHILO] Involved in the degradation of pyridoxine or pyridoxamine (free, phosphate-unbound, forms of vitamin B6). Hydrolyzes 4-pyridoxolactone to 4-pyridoxic acid. Has lower activity toward N-hexanoyl-D,L-homoserine lactone, but is not active toward 5-pyridoxolactone and gamma-butyrolactone. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
4-Pyridoxolactonase from Mesorhizobium loti catalyzes the zinc-dependent lactone-ring hydrolysis of 4-pyridoxolactone (4PAL) to 4-pyridoxic acid (4PA) in vitamin B6 degradation pathway I. The crystal structures of 4-pyridoxolactonase and its complex with 5-pyridoxolactone (5PAL; the competitive inhibitor) were determined. The overall structure was an alphabeta/betaalpha sandwich fold, and two zinc ions were coordinated. This strongly suggested that the enzyme belongs to subclass B3 of the class B beta-lactamases. In the complex structure, the carbonyl group of 5PAL pointed away from the active site, revealing why it acts as a competitive inhibitor. Based on docking simulation with 4PAL, 4PA and a reaction intermediate, 4-pyridoxolactonase probably catalyzes the reaction through a subclass B2-like mechanism, not the subclass B3 mechanism. | |||
Structure of 4-pyridoxolactonase from Mesorhizobium loti.,Kobayashi J, Yoshikane Y, Yagi T, Baba S, Mizutani K, Takahashi N, Mikami B Acta Crystallogr F Struct Biol Commun. 2014 Apr;70(Pt 4):424-32. doi:, 10.1107/S2053230X14003926. Epub 2014 Mar 25. PMID:24699732<ref>PMID:24699732</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4keq" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Mesorhizobium japonicum MAFF 303099]] | |||
[[Category: Baba S]] | |||
[[Category: Kobayashi J]] | |||
[[Category: Mikami B]] | |||
[[Category: Mizutani K]] | |||
[[Category: Takahashi N]] | |||
[[Category: Yagi T]] | |||
[[Category: Yoshikane Y]] | |||
