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| | <StructureSection load='2nv9' size='340' side='right'caption='[[2nv9]], [[Resolution|resolution]] 1.95Å' scene=''> | | <StructureSection load='2nv9' size='340' side='right'caption='[[2nv9]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2nv9]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlorella_pbcv-1_virus Chlorella pbcv-1 virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NV9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2nv9]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Paramecium_bursaria_Chlorella_virus_1 Paramecium bursaria Chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NV9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 1.95Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nva|2nva]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">A207R ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10506 Chlorella PBCV-1 virus])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Arginine_decarboxylase Arginine decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.19 4.1.1.19] </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=2nv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nv9 OCA], [https://pdbe.org/2nv9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nv9 RCSB], [https://www.ebi.ac.uk/pdbsum/2nv9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nv9 ProSAT]</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=2nv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nv9 OCA], [https://pdbe.org/2nv9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nv9 RCSB], [https://www.ebi.ac.uk/pdbsum/2nv9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nv9 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q84527_PBCV1 Q84527_PBCV1] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arginine decarboxylase]] | |
| - | [[Category: Chlorella pbcv-1 virus]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Akella, R]] | + | [[Category: Paramecium bursaria Chlorella virus 1]] |
| - | [[Category: Goldsmith, E]] | + | [[Category: Akella R]] |
| - | [[Category: Phillips, M A]]
| + | [[Category: Goldsmith E]] |
| - | [[Category: Shah, R H]]
| + | [[Category: Phillips MA]] |
| - | [[Category: Eukaryotic-like odc]] | + | [[Category: Shah RH]] |
| - | [[Category: Lyase]] | + | |
| - | [[Category: Plp]] | + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
Q84527_PBCV1
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The group IV pyridoxal-5'-phosphate (PLP)-dependent decarboxylases belong to the beta/alpha barrel structural family, and include enzymes with substrate specificity for a range of basic amino acids. A unique homolog of this family, the Paramecium bursaria Chlorella virus arginine decarboxylase (cvADC), shares about 40% amino acid sequence identity with the eukaryotic ornithine decarboxylases (ODCs). The X-ray structure of cvADC has been solved to 1.95 and 1.8 A resolution for the free and agmatine (product)-bound enzymes. The global structural differences between cvADC and eukaryotic ODC are minimal (rmsd of 1.2-1.4 A); however, the active site has significant structural rearrangements. The key "specificity element," is identified as the 310-helix that contains and positions substrate-binding residues such as E296 cvADC (D332 in T. brucei ODC). In comparison to the ODC structures, the 310-helix in cvADC is shifted over 2 A away from the PLP cofactor, thus accommodating the larger arginine substrate. Within the context of this conserved fold, the protein is designed to be flexible in the positioning and amino acid sequence of the 310-helix, providing a mechanism to evolve different substrate preferences within the family without large structural rearrangements. Also, in the structure, the "K148-loop" (homologous to the "K169-loop" of ODC) is observed in a closed, substrate-bound conformation for the first time. Apparently the K148 loop is a mobile loop, analogous to those observed in triose phosphate isomerase and tryptophan synthetase. In conjunction with prior structural studies these data predict that this loop adopts different conformations throughout the catalytic cycle, and that loop movement may be kinetically linked to the rate-limiting step of product release.
X-ray structure of Paramecium bursaria Chlorella virus arginine decarboxylase: insight into the structural basis for substrate specificity.,Shah R, Akella R, Goldsmith EJ, Phillips MA Biochemistry. 2007 Mar 13;46(10):2831-41. Epub 2007 Feb 17. PMID:17305368[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shah R, Akella R, Goldsmith EJ, Phillips MA. X-ray structure of Paramecium bursaria Chlorella virus arginine decarboxylase: insight into the structural basis for substrate specificity. Biochemistry. 2007 Mar 13;46(10):2831-41. Epub 2007 Feb 17. PMID:17305368 doi:10.1021/bi6023447
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