|
|
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of pyridoxine 4-oxidase - pyridoxamine complex== | | ==Crystal structure of pyridoxine 4-oxidase - pyridoxamine complex== |
| - | <StructureSection load='4ha6' size='340' side='right' caption='[[4ha6]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='4ha6' size='340' side='right'caption='[[4ha6]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ha6]] 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=4HA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HA6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ha6]] 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=4HA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HA6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PXM:4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL'>PXM</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PXM:4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL'>PXM</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</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=4ha6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ha6 OCA], [https://pdbe.org/4ha6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ha6 RCSB], [https://www.ebi.ac.uk/pdbsum/4ha6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ha6 ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3t37|3t37]]</td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mll6785, pno ([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/Pyridoxine_4-oxidase Pyridoxine 4-oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.12 1.1.3.12] </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=4ha6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ha6 OCA], [http://pdbe.org/4ha6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ha6 RCSB], [http://www.ebi.ac.uk/pdbsum/4ha6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ha6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q5NT46_RHILI Q5NT46_RHILI] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
Line 22: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 33669]] | + | [[Category: Large Structures]] |
| - | [[Category: Pyridoxine 4-oxidase]] | + | [[Category: Mesorhizobium loti]] |
| - | [[Category: Kobayashi, J]] | + | [[Category: Kobayashi J]] |
| - | [[Category: Mikami, B]] | + | [[Category: Mikami B]] |
| - | [[Category: Mugo, A N]] | + | [[Category: Mugo AN]] |
| - | [[Category: Yagi, T]] | + | [[Category: Yagi T]] |
| - | [[Category: Adp binding]]
| + | |
| - | [[Category: Beta alpha beta fold]]
| + | |
| - | [[Category: Fad binding domain]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Substrate access tunnel]]
| + | |
| - | [[Category: Substrate binding domain]]
| + | |
| Structural highlights
Function
Q5NT46_RHILI
Publication Abstract from PubMed
Pyridoxine 4-oxidase (PNOX) from Mesorhizobium loti is a monomeric glucose-methanol-choline (GMC) oxidoreductase family enzyme, catalyzes FAD-dependent oxidation of pyridoxine (PN) into pyridoxal, and is the first enzyme in pathway I for the degradation of PN. The tertiary structures of PNOX with a C-terminal His6-tag and PNOX-pyridoxamine (PM) complex were determined at 2.2A and at 2.1A resolutions, respectively. The overall structure consisted of FAD-binding and substrate-binding domains. In the active site, His460, His462, and Pro504 were located on the re-face of the isoalloxazine ring of FAD. PM binds to the active site through several hydrogen bonds. The side chains of His462 and His460 are located at 2.7 and 3.1A from the N4' atom of PM. The activities of His460Ala and His462Ala mutant PNOXs were very low, and 460Ala/His462Ala double mutant PNOX exhibited no activity. His462 may act as a general base for the abstraction of a proton from the 4'-hydroxyl of PN. His460 may play a role in the binding and positioning of PN. The C4' atom in PM is located at 3.2A, and the hydride ion from the C4' atom may be transferred to the N5 atom of the isoalloxazine ring. The comparison of active site residues in GMC oxidoreductase shows that Pro504 in PNOX corresponds to Asn or His of the conserved His-Asn or His-His pair in other GMC oxidoreductases. The function of the novel proline residue was discussed.
Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti.,Mugo AN, Kobayashi J, Yamasaki T, Mikami B, Ohnishi K, Yoshikane Y, Yagi T Biochim Biophys Acta. 2013 Jun;1834(6):953-63. doi: 10.1016/j.bbapap.2013.03.004., Epub 2013 Mar 15. PMID:23501672[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Mugo AN, Kobayashi J, Yamasaki T, Mikami B, Ohnishi K, Yoshikane Y, Yagi T. Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti. Biochim Biophys Acta. 2013 Jun;1834(6):953-63. doi: 10.1016/j.bbapap.2013.03.004., Epub 2013 Mar 15. PMID:23501672 doi:10.1016/j.bbapap.2013.03.004
|
