1S2B

Structure of SCP-B the first member of the Eqolisin family of Peptidases to have its structure determined

1S2B の概要

• エントリーDOI: 10.2210/pdb1s2b/pdb
• 関連するPDBエントリー: 1s2k
• 分子名称: Scytalidopepsin B (2 entities in total)
• 機能のキーワード: beta sandwich, carboxyl peptidase, protease, proteinase, eqolisin family, hydrolase
• 由来する生物種: Scytalidium lignicola
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 21553.81

構造登録者

Fujinaga, M.,Cherney, M.M.,Oyama, H.,Oda, K.,James, M.N. (登録日: 2004-01-08, 公開日: 2004-04-27, 最終更新日: 2024-10-30)

主引用文献

Fujinaga, M.,Cherney, M.M.,Oyama, H.,Oda, K.,James, M.N.
The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium lignicolum
Proc.Natl.Acad.Sci.USA, 101:3364-3369, 2004

PubMed Abstract: The molecular structure of the pepstatin-insensitive carboxyl peptidase from Scytalidium lignicolum, formerly known as scytalidopepsin B, was solved by multiple isomorphous replacement phasing methods and refined to an R factor of 0.230 (R(free) = 0.246) at 2.1-A resolution. In addition to the structure of the unbound peptidase, the structure of a product complex of cleaved angiotensin II bound in the active site of the enzyme was also determined. We propose the name scytalidocarboxyl peptidase B (SCP-B) for this enzyme. On the basis of conserved, catalytic residues identified at the active site, we suggest the name Eqolisin for the enzyme family. The previously uninvestigated SCP-B fold is that of a beta-sandwich; each sheet has seven antiparallel strands. A tripeptide product, Ala-Ile-His, bound in the active site of SCP-B has allowed for identification of the catalytic residues and the residues in subsites S1, S2, and S3, which are important for substrate binding. The most likely hydrolytic mechanism involves nucleophilic attack of a general base (Glu-136)-activated water (OH(-)) on the si-face of the scissile peptide carbonylcarbon atom to form a tetrahedral intermediate. Electrophilic assistance and oxyanion stabilization is provided by the side-chain amide of Gln-53. Protonation of the leaving-group nitrogen is accomplished by the general acid function of the protonated carboxyl group of Glu-136.

PubMed: 14993599
DOI: 10.1073/pnas.0400246101

実験手法

X-RAY DIFFRACTION (2.1 Å)