|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of wild type tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti== | | ==Crystal structure of wild type tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti== |
| - | <StructureSection load='3nug' size='340' side='right' caption='[[3nug]], [[Resolution|resolution]] 1.79Å' scene=''> | + | <StructureSection load='3nug' size='340' side='right'caption='[[3nug]], [[Resolution|resolution]] 1.79Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3nug]] is a 4 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=3NUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NUG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3nug]] is a 4 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=3NUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NUG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.788Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mlr6807, pldh-t ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381 ATCC 33669])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_4-dehydrogenase Pyridoxal 4-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.107 1.1.1.107] </span></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=3nug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nug OCA], [https://pdbe.org/3nug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nug RCSB], [https://www.ebi.ac.uk/pdbsum/3nug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nug ProSAT]</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=3nug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nug OCA], [http://pdbe.org/3nug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nug RCSB], [http://www.ebi.ac.uk/pdbsum/3nug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nug ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PLDH_RHILO PLDH_RHILO]] Involved in the degradation of pyridoxine or pyridoxamine (free, phosphate-unbound, forms of vitamin B6). Oxidizes pyridoxal to 4-pyridoxolactone, but does not have activity toward pyridoxal 5'-phosphate, pyridoxine, pyridoxamine, pyridoxamine 5'-phosphate, 4-phthalaldehyde, 2-nitrobenzaldehyde, pyridine, formaldehyde, 2-carboxybenzaldehyde or sugars.<ref>PMID:16824480</ref> | + | [https://www.uniprot.org/uniprot/PLDH_RHILO PLDH_RHILO] Involved in the degradation of pyridoxine or pyridoxamine (free, phosphate-unbound, forms of vitamin B6). Oxidizes pyridoxal to 4-pyridoxolactone, but does not have activity toward pyridoxal 5'-phosphate, pyridoxine, pyridoxamine, pyridoxamine 5'-phosphate, 4-phthalaldehyde, 2-nitrobenzaldehyde, pyridine, formaldehyde, 2-carboxybenzaldehyde or sugars.<ref>PMID:16824480</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 33669]] | + | [[Category: Large Structures]] |
| - | [[Category: Pyridoxal 4-dehydrogenase]] | + | [[Category: Mesorhizobium loti]] |
| - | [[Category: Chu, H N]] | + | [[Category: Chu HN]] |
| - | [[Category: 4-pyridoxolactone]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Pyridoxal]]
| + | |
| - | [[Category: Short chain dehydrogenase/reductase]]
| + | |
| - | [[Category: Tpldh]]
| + | |
| Structural highlights
Function
PLDH_RHILO Involved in the degradation of pyridoxine or pyridoxamine (free, phosphate-unbound, forms of vitamin B6). Oxidizes pyridoxal to 4-pyridoxolactone, but does not have activity toward pyridoxal 5'-phosphate, pyridoxine, pyridoxamine, pyridoxamine 5'-phosphate, 4-phthalaldehyde, 2-nitrobenzaldehyde, pyridine, formaldehyde, 2-carboxybenzaldehyde or sugars.[1]
Publication Abstract from PubMed
Pyridoxal 4-dehydrogenase catalyzes the irreversible oxidation of pyridoxal to 4-pyridoxolactone and is involved in degradation pathway I of pyridoxine, a vitamin B(6) compound. Its crystal structure was elucidated for the first time. Molecular replacement with (S)-1-phenylthanol dehydrogenase (PDB code 2EW8) was adopted to determine the tertiary structure of the NAD(+)-bound enzyme.
The crystal structure of SDR-type pyridoxal 4-dehydrogenase of Mesorhizobium loti.,Chu HN, Kobayashi J, Mikami B, Yagi T Biosci Biotechnol Biochem. 2011;75(2):388-90. Epub 2011 Feb 7. PMID:21307574[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yokochi N, Nishimura S, Yoshikane Y, Ohnishi K, Yagi T. Identification of a new tetrameric pyridoxal 4-dehydrogenase as the second enzyme in the degradation pathway for pyridoxine in a nitrogen-fixing symbiotic bacterium, Mesorhizobium loti. Arch Biochem Biophys. 2006 Aug 1;452(1):1-8. Epub 2006 Jun 16. PMID:16824480 doi:http://dx.doi.org/10.1016/j.abb.2006.06.002
- ↑ Chu HN, Kobayashi J, Mikami B, Yagi T. The crystal structure of SDR-type pyridoxal 4-dehydrogenase of Mesorhizobium loti. Biosci Biotechnol Biochem. 2011;75(2):388-90. Epub 2011 Feb 7. PMID:21307574
|
