4kep: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
New page: '''Unreleased structure''' The entry 4kep is ON HOLD Authors: Kobayashi, J., Yoshikane, Y., Baba, S., Mizutani, K., Takahashi, N., Mikami, B., Yagi, T Description: Crystal structure of...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(8 intermediate revisions by the same user not shown)
Line 1: Line 1:
'''Unreleased structure'''


The entry 4kep is ON HOLD
==Crystal structure of 4-pyridoxolactonase, wild-type==
<StructureSection load='4kep' size='340' side='right'caption='[[4kep]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
== Structural highlights ==
<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.83&#8491;</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='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>
</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.


Authors: Kobayashi, J., Yoshikane, Y., Baba, S., Mizutani, K., Takahashi, N., Mikami, B., Yagi, T
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>


Description: Crystal structure of 4-pyridoxolactonase, wild-type
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4kep" 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]]
Retrieved from "https://proteopedia.org/4kep"