1SIO

Structure of Kumamolisin-As complexed with a covalently-bound inhibitor, AcIPF

1SIO の概要

• エントリーDOI: 10.2210/pdb1sio/pdb
• 関連するPDBエントリー: 1SIU
• 関連するBIRD辞書のPRD_ID: PRD_000240
• 分子名称: kumamolisin-As, Ace-ILE-PRO-PHL peptide inhibitor, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: kumamolisin-as, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• 由来する生物種: Alicyclobacillus sendaiensis; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 111726.05

構造登録者

Li, M.,Wlodawer, A.,Gustchina, A.,Tsuruoka, N.,Ashida, M.,Minakata, H.,Oyama, H.,Oda, K.,Nishino, T.,Nakayama, T. (登録日: 2004-03-01, 公開日: 2004-03-30, 最終更新日: 2023-08-23)

主引用文献

Wlodawer, A.,Li, M.,Gustchina, A.,Tsuruoka, N.,Ashida, M.,Minakata, H.,Oyama, H.,Oda, K.,Nishino, T.,Nakayama, T.
Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity
J.Biol.Chem., 279:21500-21510, 2004

PubMed Abstract: Kumamolisin-As (previously called ScpA) is the first known example of a collagenase from the sedolisin family (MEROPS S53). This enzyme is active at low pH and in elevated temperatures. In this study that used x-ray crystallographic and biochemical methods, we investigated the structural basis of the preference of this enzyme for collagen and the importance of a glutamate residue in the unique catalytic triad (Ser(278)-Glu(78)-Asp(82)) for enzymatic activity. Crystal structures of the uninhibited enzyme and its complex with a covalently bound inhibitor, N-acetyl-isoleucyl-prolyl-phenylalaninal, showed the occurrence of a narrow S2 pocket and a groove that encompasses the active site and is rich in negative charges. Limited endoproteolysis studies of bovine type-I collagen as well as kinetic studies using peptide libraries randomized at P1 and P1', showed very strong preference for arginine at the P1 position, which correlated very well with the presence of a negatively charged residue in the S1 pocket of the enzyme. All of these features, together with those predicted through comparisons with fiddler crab collagenase, a serine peptidase, rationalize the enzyme's preference for collagen. A comparison of the Arrhenius plots of the activities of kumamolisin-As with either collagen or peptides as substrates suggests that collagen should be relaxed before proteolysis can occur. The E78H mutant, in which the catalytic triad was engineered to resemble that of subtilisin, showed only 0.01% activity of the wild-type enzyme, and its structure revealed that Ser(278), His(78), and Asp(82) do not interact with each other; thus, the canonical catalytic triad is disrupted.

PubMed: 15014068
DOI: 10.1074/jbc.M401141200

実験手法

X-RAY DIFFRACTION (1.8 Å)