EzCatDB: S00374

DB codeS00374
RLCP classification1.13.30000.10
CATH domainDomain 13.40.50.1820Catalytic domain
E.C.3.4.16.6
CSA1bcr
MACiEM0005

CATH domainRelated DB codes (homologues)
3.40.50.1820S00544,S00344,S00517,S00525,S00526,S00720,S00723,S00724,S00725,S00919,S00057,S00345,S00347,S00348,S00346,S00350,S00352,S00353,S00355,S00356,S00358,D00189,D00210,D00539,T00253

Enzyme Name
Swiss-protKEGG

P08819
Protein nameSerine carboxypeptidase 2carboxypeptidase D
cereal serine carboxypeptidase II
Saccharomyces cerevisiae KEX1 gene product
carboxypeptidase Kex1
gene KEX1 serine carboxypeptidase
KEX1 carboxypeptidase
KEX1 proteinase
KEX1DELTAp
CPDW-II
serine carboxypeptidase
Phaseolus proteinase
SynonymsEC 3.4.16.6
Serine carboxypeptidase II
Carboxypeptidase D
CPDW-II
CP-WII
ContainsSerine carboxypeptidase 2 chain A Serine carboxypeptidase II chain A
Serine carboxypeptidase 2 chain B Serine carboxypeptidase II chain B


Swiss-prot:Accession NumberP08819
Entry nameCBP2_WHEAT
ActivityPreferential release of a C-terminal arginine or lysine residue.
SubunitCarboxypeptidase II is a dimer, where each monomer is composed of two chains linked by a disulfide bond.
Subcellular location
Cofactor


SubstratesProductsintermediates
KEGG-idC00012C00001C00012C00062C00047I00087I00085I00086
CompoundPeptideH2OPeptideL-ArginineL-LysinePeptidyl-tetrahedral intermediateAcyl-enzymeTetrahedral intermediate
Typepeptide/proteinH2Opeptide/proteinamino acids,amine group,imine group,lipidamino acids,amine group,lipid


1bcrAUnbound
UnboundBound:ARG 426(chain D)UnboundUnboundUnboundIntermediate-analogue:AIP
1bcsAUnbound
UnboundBound:ARG 426(chain D)UnboundUnboundUnboundIntermediate-analogue:CST
1whsAUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1whtAUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:BZS
3sc2AUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1bcrBUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1bcsBUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1whsBUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1whtBUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3sc2BUnbound
UnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
pdbCatalytic residuesMain-chain involved in catalysis
1bcrASER 146
GLY 53;TYR 147
1bcsASER 146
GLY 53;TYR 147
1whsASER 146
GLY 53;TYR 147
1whtASER 146
GLY 53;TYR 147
3sc2ASER 146
GLY 53;TYR 147
1bcrBASP 338;HIS 397

1bcsBASP 338;HIS 397

1whsBASP 338;HIS 397

1whtBASP 338;HIS 397

3sc2BASP 338;HIS 397


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.9801-9802
[3]p.11132-11134, Scheme 1
[4]p.719-720, p.722-723

references
[1]
CommentsX-ray crystallography (3.5 Angstroms)
Medline ID90216664
PubMed ID2324088
JournalJ Biol Chem
Year1990
Volume265
Pages6528-31
AuthorsLiao DI, Remington SJ
TitleStructure of wheat serine carboxypeptidase II at 3.5-A resolution. A new class of serine proteinase.
Related Swiss-protP08819
[2]
CommentsX-ray crystallography (2.2 Angstroms)
PubMed ID1390755
JournalBiochemistry
Year1992
Volume31
Pages9796-812
AuthorsLiao DI, Breddam K, Sweet RM, Bullock T, Remington SJ
TitleRefined atomic model of wheat serine carboxypeptidase II at 2.2-A resolution.
Related PDB3sc2
[3]
CommentsX-ray crystallography (2.0 Angstroms)
PubMed ID7727364
JournalBiochemistry
Year1994
Volume33
Pages11127-34
AuthorsBullock TL, Branchaud B, Remington SJ
TitleStructure of the complex of L-benzylsuccinate with wheat serine carboxypeptidase II at 2.0-A resolution.
Related PDB1whs,1wht
[4]
CommentsX-ray crystallography (2.1/2.5 Angstroms)
PubMed ID863697
JournalJ Mol Biol
Year1996
Volume255
Pages714-25
AuthorsBullock TL, Breddam K, Remington SJ
TitlePeptide aldehyde complexes with wheat serine carboxypeptidase II: implications for the catalytic mechanism and substrate specificity.
Related PDB1bcr,1bcs

comments
This enzyme belongs to the peptidase family-S10.
According to the literature [2], [3] & [4], this enzyme has got a catalytic triad, Ser146/His397/Asp338, and an oxyainon hole, made of the backbone amides of Tyr147 and Gly53. Thus, this enzyme also performs two-step reaction, acylation and deacylation, like other serine hydrolases.
Ser146 acts as a nucleophile to attack on the carbonyl carbon atom to form an acyl-enzyme intermediate in the acylation process.
Meanwhile, an Asp-His pair acts to deprotonate the hydroxyl of the catalytic serine to make it nucleophilic. In this pair of residues, a strong electrostatic interaction between the sidechains stabilizes the imidazolium cation developed during the catalysis, according to the paper [2].
Although the catalytic mechanism of this enzyme is very similar to those of other serine hydrolases, it has several distinct features (see [3] & [4]).
Firstly, according to the paper [3], a C-terminal carboxylate of the substrate might atc as a proton sink for the catalytic His397. Here, in an acid-base preequilibrium, transfer of a proton from the protonated histidine to the substrate carboxylate neutralizes both the residue itself and the substrate, and then the conventional mechanism of serine hydrolases can proceed [3]. For this preequilibrium, the interaction of Glu145 with the substrate carboxylate might play an important role in the transition state [3].
Secondly, the stereochemistry of an enzymatic reaction seems to be opposite to that of other serine hydrolases, such as proteinase A (see [4]). This dissimilarity can distinguish these enzymes which have such a catalytic triad, Ser/His/Asp, in terms of evolution [4].

createdupdated
2002-07-042011-02-16
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.