4keq
From Proteopedia
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| - | {{STRUCTURE_4keq| PDB=4keq | SCENE= }} | ||
| - | ===Crystal structure of 4-pyridoxolactonase, 5-pyridoxolactone bound=== | ||
| - | == | + | ==Crystal structure of 4-pyridoxolactonase, 5-pyridoxolactone bound== |
| - | [[http://www.uniprot.org/uniprot/PDLA_RHILO PDLA_RHILO | + | <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> | |
| - | + | ||
| - | [[Category: | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | [[Category: Baba | + | </div> |
| - | [[Category: Kobayashi | + | <div class="pdbe-citations 4keq" style="background-color:#fffaf0;"></div> |
| - | [[Category: Mikami | + | == References == |
| - | [[Category: Mizutani | + | <references/> |
| - | [[Category: Takahashi | + | __TOC__ |
| - | [[Category: Yagi | + | </StructureSection> |
| - | [[Category: Yoshikane | + | [[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]] | ||
Current revision
Crystal structure of 4-pyridoxolactonase, 5-pyridoxolactone bound
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