3aj3: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
(5 intermediate revisions by the same user not shown)
Line 1: Line 1:


==Crystal structure of selenomethionine substituted 4-pyridoxolactonase from Mesorhizobium loti==
==Crystal structure of selenomethionine substituted 4-pyridoxolactonase from Mesorhizobium loti==
<StructureSection load='3aj3' size='340' side='right' caption='[[3aj3]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
<StructureSection load='3aj3' size='340' side='right'caption='[[3aj3]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3aj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33669 Atcc 33669]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AJ3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3aj3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AJ3 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.577&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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">[[3aj0|3aj0]]</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=3aj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aj3 OCA], [https://pdbe.org/3aj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aj3 RCSB], [https://www.ebi.ac.uk/pdbsum/3aj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aj3 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=381 ATCC 33669])</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=3aj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aj3 OCA], [http://pdbe.org/3aj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3aj3 RCSB], [http://www.ebi.ac.uk/pdbsum/3aj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3aj3 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;">
== 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3aj3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 4-pyridoxolactonase]]
[[Category: Large Structures]]
[[Category: Atcc 33669]]
[[Category: Mesorhizobium loti]]
[[Category: Baba, S]]
[[Category: Baba S]]
[[Category: Kobayashi, J]]
[[Category: Kobayashi J]]
[[Category: Mikami, B]]
[[Category: Mikami B]]
[[Category: Yagi, T]]
[[Category: Yagi T]]
[[Category: Yoshikane, Y]]
[[Category: Yoshikane Y]]
[[Category: Hydrolase]]
[[Category: Metallo-beta-lactamase]]
[[Category: Zn-protein]]
Retrieved from "https://proteopedia.org/3aj3"