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| | <StructureSection load='4wy0' size='340' side='right'caption='[[4wy0]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='4wy0' size='340' side='right'caption='[[4wy0]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4wy0]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Geoka Geoka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WY0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WY0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4wy0]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WY0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WY0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</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]] 2.3Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3ZL:N~6~-[(1Z)-4-AMINO-3-OXOPENTA-1,4-DIEN-1-YL]-L-LYSINE'>3ZL</scene>, <scene name='pdbligand=L5P:(2S)-2-AZANYL-6-[[(3R,4R)-3,4-BIS(OXIDANYL)-2-OXIDANYLIDENE-5-PHOSPHONOOXY-PENTYL]AMINO]HEXANOIC+ACID'>L5P</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3ZL:N~6~-[(1Z)-4-AMINO-3-OXOPENTA-1,4-DIEN-1-YL]-L-LYSINE'>3ZL</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=L5P:(2S)-2-AZANYL-6-[[(3R,4R)-3,4-BIS(OXIDANYL)-2-OXIDANYLIDENE-5-PHOSPHONOOXY-PENTYL]AMINO]HEXANOIC+ACID'>L5P</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4wxy|4wxy]], [[4wxz|4wxz]]</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=4wy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wy0 OCA], [https://pdbe.org/4wy0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wy0 RCSB], [https://www.ebi.ac.uk/pdbsum/4wy0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wy0 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pdxS, GK0011 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])</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=4wy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wy0 OCA], [http://pdbe.org/4wy0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wy0 RCSB], [http://www.ebi.ac.uk/pdbsum/4wy0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wy0 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PDXS_GEOKA PDXS_GEOKA]] Involved in the production of pyridoxal phosphate, probably by incorporating ammonia into the pyridine ring.[HAMAP-Rule:MF_01824] | + | [https://www.uniprot.org/uniprot/PDXS_GEOKA PDXS_GEOKA] Involved in the production of pyridoxal phosphate, probably by incorporating ammonia into the pyridine ring.[HAMAP-Rule:MF_01824] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Geoka]] | + | [[Category: Geobacillus kaustophilus HTA426]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Smith, A M]] | + | [[Category: Smith AM]] |
| - | [[Category: Smith, J L]] | + | [[Category: Smith JL]] |
| - | [[Category: Glutamine amidotransferase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Pyridoxal 5-phosphate]]
| + | |
| - | [[Category: Vitamin b6]]
| + | |
| Structural highlights
4wy0 is a 12 chain structure with sequence from Geobacillus kaustophilus HTA426. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.3Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PDXS_GEOKA Involved in the production of pyridoxal phosphate, probably by incorporating ammonia into the pyridine ring.[HAMAP-Rule:MF_01824]
Publication Abstract from PubMed
PLP synthase (PLPS) is a remarkable single-enzyme biosynthetic pathway that produces pyridoxal 5'-phosphate (PLP) from glutamine, ribose 5-phosphate (R5P) and glyceraldehyde 3-phosphate (G3P). The intact enzyme includes 12 synthase and 12 glutaminase subunits. PLP synthesis occurs in the synthase active site by a complicated mechanism involving at least two covalent intermediates at a catalytic lysine. The first intermediate forms with R5P. The glutaminase subunit is a glutamine amidotransferase that hydrolyzes glutamine and channels ammonia to the synthase active site. Ammonia attack on the first covalent intermediate forms the second intermediate. G3P reacts with the second intermediate to form PLP. To investigate the mechanism of the synthase subunit, crystal structures were obtained for three intermediate states of the Geobacillus stearothermophilus intact PLPS or its synthase subunit. The structures capture the synthase active site at three distinct steps in its complicated catalytic cycle, provide insights into the elusive mechanism, and illustrate the coordinated motions within the synthase subunit that separate the catalytic states. In the intact PLPS with a Michaelis-like intermediate in the glutaminase active site, the first covalent intermediate of the synthase is fully sequestered within the enzyme by the ordering of a generally disordered, 20-residue C-terminal tail. Following addition of ammonia, the synthase active site opens and admits the Lys149 side chain, which participates in formation of the second intermediate and PLP. Roles are identified for conserved Asp24 in the formation of the first intermediate and for conserved Arg147 in the conversion of the first to the second intermediate.
Crystal Structures Capture Three States in the Catalytic Cycle of a Pyridoxal Phosphate (PLP) Synthase.,Smith AM, Brown WC, Harms E, Smith JL J Biol Chem. 2015 Jan 7. pii: jbc.M114.626382. PMID:25568319[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Smith AM, Brown WC, Harms E, Smith JL. Crystal Structures Capture Three States in the Catalytic Cycle of a Pyridoxal Phosphate (PLP) Synthase. J Biol Chem. 2015 Jan 7. pii: jbc.M114.626382. PMID:25568319 doi:http://dx.doi.org/10.1074/jbc.M114.626382
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