2nv9: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:2nv9.gif|left|200px]] | [[Image:2nv9.gif|left|200px]] | ||
'''The X-ray Crystal Structure of the Paramecium bursaria Chlorella virus arginine decarboxylase''' | {{Structure | ||
|PDB= 2nv9 |SIZE=350|CAPTION= <scene name='initialview01'>2nv9</scene>, resolution 1.950Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=PLP:PYRIDOXAL-5'-PHOSPHATE'>PLP</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Arginine_decarboxylase Arginine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.19 4.1.1.19] | |||
|GENE= A207R ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10506 Paramecium bursaria Chlorella virus 1]) | |||
}} | |||
'''The X-ray Crystal Structure of the Paramecium bursaria Chlorella virus arginine decarboxylase''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
2NV9 is a [ | 2NV9 is a [[Single protein]] structure of sequence from [http://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]. | ||
==Reference== | ==Reference== | ||
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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/17305368 17305368] | ||
[[Category: Arginine decarboxylase]] | [[Category: Arginine decarboxylase]] | ||
[[Category: Paramecium bursaria chlorella virus 1]] | [[Category: Paramecium bursaria chlorella virus 1]] | ||
| Line 24: | Line 33: | ||
[[Category: tim barrel]] | [[Category: tim barrel]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:51:34 2008'' | ||
Revision as of 18:51, 20 March 2008
| |||||||
| , resolution 1.950Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | A207R (Paramecium bursaria Chlorella virus 1) | ||||||
| Activity: | Arginine decarboxylase, with EC number 4.1.1.19 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The X-ray Crystal Structure of the Paramecium bursaria Chlorella virus arginine decarboxylase
OverviewOverview
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.
About this StructureAbout this Structure
2NV9 is a Single protein structure of sequence from Paramecium bursaria chlorella virus 1. Full crystallographic information is available from OCA.
ReferenceReference
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
Page seeded by OCA on Thu Mar 20 17:51:34 2008