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| | <StructureSection load='4wxz' size='340' side='right'caption='[[4wxz]], [[Resolution|resolution]] 2.70Å' scene=''> | | <StructureSection load='4wxz' size='340' side='right'caption='[[4wxz]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4wxz]] is a 6 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=4WXZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WXZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4wxz]] is a 6 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=4WXZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WXZ FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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=LRK:(2S)-2-AZANYL-6-[[(2R,4R)-1,4-BIS(OXIDANYL)-3-OXIDANYLIDENE-5-PHOSPHONOOXY-PENTAN-2-YL]AMINO]HEXANOIC+ACID'>LRK</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=LRK:(2S)-2-AZANYL-6-[[(2R,4R)-1,4-BIS(OXIDANYL)-3-OXIDANYLIDENE-5-PHOSPHONOOXY-PENTAN-2-YL]AMINO]HEXANOIC+ACID'>LRK</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4wy0|4wy0]]</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=4wxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wxz OCA], [https://pdbe.org/4wxz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wxz RCSB], [https://www.ebi.ac.uk/pdbsum/4wxz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wxz 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=4wxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wxz OCA], [http://pdbe.org/4wxz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wxz RCSB], [http://www.ebi.ac.uk/pdbsum/4wxz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wxz 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: Beta/alpha barrel]]
| + | |
| - | [[Category: Glutamine amidotransferase]]
| + | |
| - | [[Category: Pyridoxal 5-phosphate]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Vitamin b6]]
| + | |
| 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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