|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Native structure of cystathionine gamma lyase (XometC) from xanthomonas oryzae pv. oryzae at pH 9.0== | | ==Native structure of cystathionine gamma lyase (XometC) from xanthomonas oryzae pv. oryzae at pH 9.0== |
| - | <StructureSection load='4ixz' size='340' side='right' caption='[[4ixz]], [[Resolution|resolution]] 2.07Å' scene=''> | + | <StructureSection load='4ixz' size='340' side='right'caption='[[4ixz]], [[Resolution|resolution]] 2.07Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ixz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanor Xanor]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3nmy 3nmy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IXZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IXZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ixz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_oryzae_pv._oryzae_KACC_10331 Xanthomonas oryzae pv. oryzae KACC 10331]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3nmy 3nmy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IXZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IXZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.07Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IT1:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>IT1</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ixs|4ixs]], [[4iy7|4iy7]], [[4iyo|4iyo]]</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=4ixz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ixz OCA], [https://pdbe.org/4ixz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ixz RCSB], [https://www.ebi.ac.uk/pdbsum/4ixz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ixz ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">metB, XOCGL, XOO0778 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=291331 XANOR])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cystathionine_gamma-lyase Cystathionine gamma-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.1 4.4.1.1] </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=4ixz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ixz OCA], [http://pdbe.org/4ixz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ixz RCSB], [http://www.ebi.ac.uk/pdbsum/4ixz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ixz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q5H4T8_XANOR Q5H4T8_XANOR] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cystathionine gamma-lyase]] | + | [[Category: Large Structures]] |
| - | [[Category: Xanor]] | + | [[Category: Xanthomonas oryzae pv. oryzae KACC 10331]] |
| - | [[Category: Kang, L W]] | + | [[Category: Kang LW]] |
| - | [[Category: Kim, J K]] | + | [[Category: Kim JK]] |
| - | [[Category: Ngo, H P.T]] | + | [[Category: Ngo HPT]] |
| - | [[Category: Cys-met metabolism plp dependent enzyme]]
| + | |
| - | [[Category: Cystathionine gamma lyase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Native]]
| + | |
| - | [[Category: Plp binding]]
| + | |
| - | [[Category: Plp dependent enzyme]]
| + | |
| - | [[Category: Xocgl]]
| + | |
| Structural highlights
Function
Q5H4T8_XANOR
Publication Abstract from PubMed
Numerous enzymes, such as the pyridoxal 5'-phosphate (PLP)-dependent enzymes, require cofactors for their activities. Using X-ray crystallography, structural snapshots of the L-serine dehydratase catalytic reaction of a bacterial PLP-dependent enzyme were determined. In the structures, the dihedral angle between the pyridine ring and the Schiff-base linkage of PLP varied from 18 degrees to 52 degrees . It is proposed that the organic cofactor PLP directly catalyzes reactions by active conformational changes, and the novel catalytic mechanism involving the PLP cofactor was confirmed by high-level quantum-mechanical calculations. The conformational change was essential for nucleophilic attack of the substrate on PLP, for concerted proton transfer from the substrate to the protein and for directing carbanion formation of the substrate. Over the whole catalytic cycle, the organic cofactor catalyzes a series of reactions, like the enzyme. The conformational change of the PLP cofactor in catalysis serves as a starting point for identifying the previously unknown catalytic roles of organic cofactors.
PLP undergoes conformational changes during the course of an enzymatic reaction.,Ngo HP, Cerqueira NM, Kim JK, Hong MK, Fernandes PA, Ramos MJ, Kang LW Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):596-606. doi:, 10.1107/S1399004713031283. Epub 2014 Jan 31. PMID:24531493[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ngo HP, Cerqueira NM, Kim JK, Hong MK, Fernandes PA, Ramos MJ, Kang LW. PLP undergoes conformational changes during the course of an enzymatic reaction. Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):596-606. doi:, 10.1107/S1399004713031283. Epub 2014 Jan 31. PMID:24531493 doi:http://dx.doi.org/10.1107/S1399004713031283
|
