1S2B

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

Summary for 1S2B

• Entry DOI: 10.2210/pdb1s2b/pdb
• Related: 1s2k
• Descriptor: Scytalidopepsin B (2 entities in total)
• Functional Keywords: beta sandwich, carboxyl peptidase, protease, proteinase, eqolisin family, hydrolase
• Biological source: Scytalidium lignicola
• Total number of polymer chains: 1
• Total formula weight: 21553.81

Authors

Fujinaga, M.,Cherney, M.M.,Oyama, H.,Oda, K.,James, M.N. (deposition date: 2004-01-08, release date: 2004-04-27, Last modification date: 2024-10-30)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.1 Å)