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| | ==PLPS (inactive glutaminase mutant) co-crystallized with glutamine and R5P.== | | ==PLPS (inactive glutaminase mutant) co-crystallized with glutamine and R5P.== |
| - | <StructureSection load='4wxy' size='340' side='right' caption='[[4wxy]], [[Resolution|resolution]] 2.70Å' scene=''> | + | <StructureSection load='4wxy' size='340' side='right'caption='[[4wxy]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4wxy]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WXY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WXY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4wxy]] 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=4WXY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WXY FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYG:2-AMINO-4-(AMINO-3-OXO-PROPYLSULFANYLCARBONYL)-BUTYRIC+ACID'>CYG</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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4wy0|4wy0]], [[4wxz|4wxz]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYG:2-AMINO-4-(AMINO-3-OXO-PROPYLSULFANYLCARBONYL)-BUTYRIC+ACID'>CYG</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='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=4wxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wxy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wxy RCSB], [http://www.ebi.ac.uk/pdbsum/4wxy PDBsum]</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=4wxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wxy OCA], [https://pdbe.org/4wxy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wxy RCSB], [https://www.ebi.ac.uk/pdbsum/4wxy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wxy 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] [[http://www.uniprot.org/uniprot/PDXT_GEOKA PDXT_GEOKA]] Involved in the hydrolysis of glutamine to glutamate and ammonia. Channels an ammonia molecule to PdxS. | + | [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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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4wxy" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Smith, A M]] | + | [[Category: Geobacillus kaustophilus HTA426]] |
| - | [[Category: Smith, J L]] | + | [[Category: Large Structures]] |
| - | [[Category: Beta/alpha barrel]] | + | [[Category: Smith AM]] |
| - | [[Category: Glutamine amidotransferase]] | + | [[Category: Smith JL]] |
| - | [[Category: Pyridoxal 5-phosphate]]
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| - | [[Category: Vitamin b6]]
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| Structural highlights
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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