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| | <StructureSection load='4kep' size='340' side='right'caption='[[4kep]], [[Resolution|resolution]] 1.83Å' scene=''> | | <StructureSection load='4kep' size='340' side='right'caption='[[4kep]], [[Resolution|resolution]] 1.83Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4kep]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_japonicum_(strain_lmg_29417_/_cect_9101_/_maff_303099) Mesorhizobium japonicum (strain lmg 29417 / cect 9101 / maff 303099)]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3aj0 3aj0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KEP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4kep]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_japonicum_MAFF_303099 Mesorhizobium japonicum MAFF 303099]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3aj0 3aj0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KEP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3aj3|3aj3]], [[4keq|4keq]]</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=4kep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kep OCA], [https://pdbe.org/4kep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kep RCSB], [https://www.ebi.ac.uk/pdbsum/4kep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kep ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mlr6805 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-pyridoxolactonase 4-pyridoxolactonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.27 3.1.1.27] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kep OCA], [http://pdbe.org/4kep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kep RCSB], [http://www.ebi.ac.uk/pdbsum/4kep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kep ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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. | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 4-pyridoxolactonase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Baba, S]] | + | [[Category: Mesorhizobium japonicum MAFF 303099]] |
| - | [[Category: Kobayashi, J]] | + | [[Category: Baba S]] |
| - | [[Category: Mikami, B]] | + | [[Category: Kobayashi J]] |
| - | [[Category: Mizutani, K]] | + | [[Category: Mikami B]] |
| - | [[Category: Takahashi, N]] | + | [[Category: Mizutani K]] |
| - | [[Category: Yagi, T]] | + | [[Category: Takahashi N]] |
| - | [[Category: Yoshikane, Y]] | + | [[Category: Yagi T]] |
| - | [[Category: Alpha-beta/beta-alpha fold]]
| + | [[Category: Yoshikane Y]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Lactone]]
| + | |
| Structural highlights
Function
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kobayashi J, Yoshikane Y, Yagi T, Baba S, Mizutani K, Takahashi N, Mikami B. Structure of 4-pyridoxolactonase from Mesorhizobium loti. Acta Crystallogr F Struct Biol Commun. 2014 Apr;70(Pt 4):424-32. doi:, 10.1107/S2053230X14003926. Epub 2014 Mar 25. PMID:24699732 doi:http://dx.doi.org/10.1107/S2053230X14003926
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