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| | ==Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus== | | ==Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus== |
| - | <StructureSection load='4fir' size='340' side='right' caption='[[4fir]], [[Resolution|resolution]] 3.10Å' scene=''> | + | <StructureSection load='4fir' size='340' side='right'caption='[[4fir]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fir]] 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=4FIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FIR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fir]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FIR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 3.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fiq|4fiq]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></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 PYRHO])</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=4fir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fir OCA], [https://pdbe.org/4fir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fir RCSB], [https://www.ebi.ac.uk/pdbsum/4fir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fir 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=4fir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fir OCA], [http://pdbe.org/4fir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fir RCSB], [http://www.ebi.ac.uk/pdbsum/4fir PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fir ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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] | + | [https://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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrho]] | + | [[Category: Large Structures]] |
| - | [[Category: Lee, H H]] | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | [[Category: Matsuura, A]] | + | [[Category: Lee HH]] |
| - | [[Category: Suh, S W]] | + | [[Category: Matsuura A]] |
| - | [[Category: Yoon, H J]] | + | [[Category: Suh SW]] |
| - | [[Category: Yoon, J Y]] | + | [[Category: Yoon HJ]] |
| - | [[Category: Lyase]] | + | [[Category: Yoon JY]] |
| - | [[Category: Pdx]]
| + | |
| - | [[Category: Pyridoxal biosynthesis lyase]]
| + | |
| - | [[Category: 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 PubMed
Pyridoxal 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
- ↑ Matsuura A, Yoon JY, Yoon HJ, Lee HH, Suh SW. Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii. Mol Cells. 2012 Oct;34(4):407-12. doi: 10.1007/s10059-012-0198-8. Epub 2012 Oct, 18. PMID:23104439 doi:http://dx.doi.org/10.1007/s10059-012-0198-8
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