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New page: left|200px<br /><applet load="2nv9" size="350" color="white" frame="true" align="right" spinBox="true" caption="2nv9, resolution 1.950Å" /> '''The X-ray Crystal S... |
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== | ==The X-ray Crystal Structure of the Paramecium bursaria Chlorella virus arginine decarboxylase== | ||
The group IV pyridoxal-5'-phosphate (PLP)-dependent decarboxylases belong | <StructureSection load='2nv9' size='340' side='right'caption='[[2nv9]], [[Resolution|resolution]] 1.95Å' scene=''> | ||
== Structural highlights == | |||
<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='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='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='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> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q84527_PBCV1 Q84527_PBCV1] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nv/2nv9_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2nv9 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:17305368</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 2nv9" style="background-color:#fffaf0;"></div> | ||
[[Category: Paramecium bursaria | == References == | ||
<references/> | |||
[[Category: Akella | __TOC__ | ||
[[Category: Goldsmith | </StructureSection> | ||
[[Category: Phillips | [[Category: Large Structures]] | ||
[[Category: Shah | [[Category: Paramecium bursaria Chlorella virus 1]] | ||
[[Category: Akella R]] | |||
[[Category: Goldsmith E]] | |||
[[Category: Phillips MA]] | |||
[[Category: Shah RH]] | |||
Latest revision as of 03:11, 28 December 2023
The X-ray Crystal Structure of the Paramecium bursaria Chlorella virus arginine decarboxylaseThe X-ray Crystal Structure of the Paramecium bursaria Chlorella virus arginine decarboxylase
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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
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