2nv9
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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 with as ligand. Active as Arginine decarboxylase, with EC number 4.1.1.19 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
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