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| | ==Crystal structure of pyridoxal kinase complexed with ADP== | | ==Crystal structure of pyridoxal kinase complexed with ADP== |
| - | <StructureSection load='1rfv' size='340' side='right' caption='[[1rfv]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='1rfv' size='340' side='right'caption='[[1rfv]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1rfv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RFV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RFV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1rfv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RFV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RFV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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]] 2.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1lhp|1lhp]], [[1lhr|1lhr]], [[1rft|1rft]], [[1rfu|1rfu]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1rfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rfv OCA], [https://pdbe.org/1rfv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rfv RCSB], [https://www.ebi.ac.uk/pdbsum/1rfv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rfv 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=1rfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rfv OCA], [http://pdbe.org/1rfv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rfv RCSB], [http://www.ebi.ac.uk/pdbsum/1rfv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rfv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PDXK_SHEEP PDXK_SHEEP]] Required for synthesis of pyridoxal-5-phosphate from vitamin B6. | + | [https://www.uniprot.org/uniprot/PDXK_SHEEP PDXK_SHEEP] Required for synthesis of pyridoxal-5-phosphate from vitamin B6. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </div> | | </div> |
| | <div class="pdbe-citations 1rfv" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1rfv" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Pyridoxal kinase|Pyridoxal kinase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Ovis aries]] | | [[Category: Ovis aries]] |
| - | [[Category: Pyridoxal kinase]]
| + | [[Category: Jiang T]] |
| - | [[Category: Jiang, T]] | + | [[Category: Li M-H]] |
| - | [[Category: Li, M H]] | + | [[Category: Liang D-C]] |
| - | [[Category: Liang, D C]] | + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PDXK_SHEEP Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
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
To understand the processes involved in the catalytic mechanism of pyridoxal kinase (PLK),1 we determined the crystal structures of PLK.AMP-PCP-pyridoxamine, PLK.ADP.PLP, and PLK.ADP complexes. Comparisons of these structures have revealed that PLK exhibits different conformations during its catalytic process. After the binding of AMP-PCP (an analogue that replaced ATP) and pyridoxamine to PLK, this enzyme retains a conformation similar to that of the PLK.ATP complex. The distance between the reacting groups of the two substrates is 5.8 A apart, indicating that the position of ATP is not favorable to spontaneous transfer of its phosphate group. However, the structure of PLK.ADP.PLP complex exhibited significant changes in both the conformation of the enzyme and the location of the ligands at the active site. Therefore, it appears that after binding of both substrates, the enzyme-substrate complex requires changes in the protein structure to enable the transfer of the phosphate group from ATP to vitamin B(6). Furthermore, a conformation of the enzyme-substrate complex before the transition state of the enzymatic reaction was also hypothesized.
Conformational changes in the reaction of pyridoxal kinase.,Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T, Liang DC J Biol Chem. 2004 Apr 23;279(17):17459-65. Epub 2004 Jan 13. PMID:14722069[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T, Liang DC. Conformational changes in the reaction of pyridoxal kinase. J Biol Chem. 2004 Apr 23;279(17):17459-65. Epub 2004 Jan 13. PMID:14722069 doi:http://dx.doi.org/10.1074/jbc.M312380200
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