2NV9

The X-ray Crystal Structure of the Paramecium bursaria Chlorella virus arginine decarboxylase

2NV9 の概要

• エントリーDOI: 10.2210/pdb2nv9/pdb
• 関連するPDBエントリー: 2NVA
• 分子名称: A207R protein, arginine decarboxylase, PYRIDOXAL-5'-PHOSPHATE (3 entities in total)
• 機能のキーワード: arginine decarboxylase, plp, tim barrel, eukaryotic-like odc, lyase
• 由来する生物種: Paramecium bursaria Chlorella virus 1
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 337841.66

構造登録者

Shah, R.H.,Akella, R.,Goldsmith, E.,Phillips, M.A. (登録日: 2006-11-11, 公開日: 2007-03-20, 最終更新日: 2023-12-27)

主引用文献

Shah, R.,Akella, R.,Goldsmith, E.J.,Phillips, M.A.
X-ray Structure of Paramecium bursaria Chlorella Virus Arginine Decarboxylase: Insight into the Structural Basis for Substrate Specificity.
Biochemistry, 46:2831-2841, 2007

PubMed Abstract: 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.

PubMed: 17305368
DOI: 10.1021/bi6023447

実験手法

X-RAY DIFFRACTION (1.95 Å)