4fiq: Difference between revisions
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==Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii== | ==Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii== | ||
<StructureSection load='4fiq' size='340' side='right' caption='[[4fiq]], [[Resolution|resolution]] 2.70Å' scene=''> | <StructureSection load='4fiq' size='340' side='right' caption='[[4fiq]], [[Resolution|resolution]] 2.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4fiq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[4fiq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrho Pyrho]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FIQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FIQ FirstGlance]. <br> | ||
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fir|4fir]]</td></tr> | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fir|4fir]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pdxS, PH1355 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pdxS, PH1355 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 PYRHO])</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=4fiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fiq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fiq RCSB], [http://www.ebi.ac.uk/pdbsum/4fiq PDBsum]</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=4fiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fiq OCA], [http://pdbe.org/4fiq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fiq RCSB], [http://www.ebi.ac.uk/pdbsum/4fiq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fiq ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[[http://www.uniprot.org/uniprot/PDXS_PYRHO PDXS_PYRHO]] Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively.[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 4fiq" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Pyrho]] | ||
[[Category: Lee, H H]] | [[Category: Lee, H H]] | ||
[[Category: Matsuura, A]] | [[Category: Matsuura, A]] | ||
Revision as of 22:55, 15 December 2016
Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshiiCrystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii
Structural highlights
Function[PDXS_PYRHO] Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively.[HAMAP-Rule:MF_01824] Publication Abstract from PubMedPyridoxal 5'-phosphate (PLP) is the biologically active form of vitamin B(6) and is de novo synthesized from three substrates, dihydroxyacetone phosphate (DHAP), riburose 5-phosphate (RBP), and ammonia hydrolysed from glutamine. Glutamine amidotransferase (PdxT) catalyzes the production of ammonia from glutamine, while PdxS catalyzes the following condensation of ribulose 5-phosphate (Ru5P), glyceraldehyde-3-phosphate (G3P), and ammonia. PdxS exists as a hexamer or dodecamer depending on species and makes a 1:1 complex with PdxT. Pyrococcus horikoshii PdxS has a 37 amino acids insertion region, which is found in some archaeal PdxS proteins, but its structure and function are unknown. To provide further structural information on the role of the insertion region, the oligomeric state, and ligand binding mode of P. horikoshii PdxS, the crystal structure of PdxS from P. horikoshii was solved in two forms: (i) apo form, (ii) r ibose 5-phosphate (R5P) complex and the quaternary structure of PdxS in solution was determined by analytical gel filtration. P. horikoshii PdxS forms hexamer in solution based on analytical gel filtration data. When we superimpose the structure of P. horikoshii PdxS with other dodecamer structures of PdxS, the additional insertion is located apart from the active site and induces a steric clash on the hexamer-hexamer interface of PdxS proteins. Our results suggest that the additional insertion perturbs dodecamer formation of P. horikoshii PdxS. Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii.,Matsuura A, Yoon JY, Yoon HJ, Lee HH, Suh SW Mol Cells. 2012 Oct;34(4):407-12. doi: 10.1007/s10059-012-0198-8. Epub 2012 Oct, 18. PMID:23104439[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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