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| | <StructureSection load='1td2' size='340' side='right'caption='[[1td2]], [[Resolution|resolution]] 2.22Å' scene=''> | | <StructureSection load='1td2' size='340' side='right'caption='[[1td2]], [[Resolution|resolution]] 2.22Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1td2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TD2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1TD2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1td2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TD2 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.22Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDXY, B1636 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </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=1td2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1td2 OCA], [https://pdbe.org/1td2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1td2 RCSB], [https://www.ebi.ac.uk/pdbsum/1td2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1td2 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1td2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1td2 OCA], [http://pdbe.org/1td2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1td2 RCSB], [http://www.ebi.ac.uk/pdbsum/1td2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1td2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PDXY_ECOLI PDXY_ECOLI]] Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxamine, but has negligible activity toward pyridoxal and pyridoxine as substrates.[HAMAP-Rule:MF_01639] | + | [https://www.uniprot.org/uniprot/PDXY_ECOLI PDXY_ECOLI] Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxamine, but has negligible activity toward pyridoxal and pyridoxine as substrates.[HAMAP-Rule:MF_01639] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/td/1td2_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/td/1td2_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyridoxal kinase]]
| + | [[Category: Hunt S]] |
| - | [[Category: Hunt, S]] | + | [[Category: Musayev FN]] |
| - | [[Category: Musayev, F N]] | + | [[Category: Safo MK]] |
| - | [[Category: Safo, M K]] | + | [[Category: Scarsdale N]] |
| - | [[Category: Salvo, M di]]
| + | [[Category: Schirch V]] |
| - | [[Category: Scarsdale, N]] | + | [[Category: Di Salvo M]] |
| - | [[Category: Schirch, V]] | + | |
| - | [[Category: Kinase]] | + | |
| - | [[Category: Pdxy]]
| + | |
| - | [[Category: Phosphorylation]]
| + | |
| - | [[Category: Ribokinase family]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PDXY_ECOLI Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxamine, but has negligible activity toward pyridoxal and pyridoxine as substrates.[HAMAP-Rule:MF_01639]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The crystal structure of Escherichia coli PdxY, the protein product of the pdxY gene, has been determined to a 2.2-A resolution. PdxY is a member of the ribokinase superfamily of enzymes and has sequence homology with pyridoxal kinases that phosphorylate pyridoxal at the C-5' hydroxyl. The protein is a homodimer with an active site on each monomer composed of residues that come exclusively from each respective subunit. The active site is filled with a density that fits that of pyridoxal. In monomer A, the ligand appears to be covalently attached to Cys122 as a thiohemiacetal, while in monomer B it is not covalently attached but appears to be partially present as pyridoxal 5'-phosphate. The presence of pyridoxal phosphate and pyridoxal as ligands was confirmed by the activation of aposerine hydroxymethyltransferase after release of the ligand by the denaturation of PdxY. The ligand, which appears to be covalently attached to Cys122, does not dissociate after denaturation of the protein. A detailed comparison (of functional properties, sequence homology, active site and ATP-binding-site residues, and active site flap types) of PdxY with other pyridoxal kinases as well as the ribokinase superfamily in general suggested that PdxY is a member of a new subclass of the ribokinase superfamily. The structure of PdxY also permitted an interpretation of work that was previously published about this enzyme.
Crystal structure of the PdxY Protein from Escherichia coli.,Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V J Bacteriol. 2004 Dec;186(23):8074-82. PMID:15547280[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V. Crystal structure of the PdxY Protein from Escherichia coli. J Bacteriol. 2004 Dec;186(23):8074-82. PMID:15547280 doi:186/23/8074
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