EzCatDB: S00408
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeS00408
RLCP classification1.13.30000.39 : Hydrolysis
CATH domainDomain 13.40.630.20 : AminopeptidaseCatalytic domain
E.C.3.4.19.3
CSA1aug


Enzyme Name
UniProtKBKEGG

O07883O73944P46107
Protein namePyrrolidone-carboxylate peptidasePyrrolidone-carboxylate peptidasePyrrolidone-carboxylate peptidasepyroglutamyl-peptidase I
5-oxoprolyl-peptidase
pyrase
pyroglutamate aminopeptidase
pyroglutamyl aminopeptidase
L-pyroglutamyl peptide hydrolase
pyrrolidone-carboxyl peptidase
pyrrolidone-carboxylate peptidase
pyrrolidonyl peptidase
L-pyrrolidonecarboxylate peptidase
pyroglutamidase
pyrrolidonecarboxylyl peptidase
SynonymsEC 3.4.19.3
5-oxoprolyl-peptidase
Pyroglutamyl-peptidase I
PGP-I
EC 3.4.19.3
5-oxoprolyl-peptidase
Pyroglutamyl-peptidase I
PGP-I
Pyrase
EC 3.4.19.3
5-oxoprolyl-peptidase
Pyroglutamyl-peptidase I
PGP-I
Pyrase
RefSeq
NP_579028.1 (Protein)
NC_003413.1 (DNA/RNA sequence)

MEROPSC15.001 (Cysteine)
C15.001 (Cysteine)
C15.001 (Cysteine)
PfamPF01470 (Peptidase_C15)
[Graphical view]
PF01470 (Peptidase_C15)
[Graphical view]
PF01470 (Peptidase_C15)
[Graphical view]


UniProtKB:Accession NumberO07883O73944P46107
Entry namePCP_THELIPCP_PYRFUPCP_BACAM
ActivityRelease of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro.Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro.Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro.
SubunitHomotetramer.Homotetramer made of two disulfide-linked dimers.Homotetramer.
Subcellular locationCytoplasm.Cytoplasm.Cytoplasm.
Cofactor



Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00017C00012C00001C00017C00012I00153I00154I00155
CompoundProteinPeptideH2OProteinPeptidePeptidyl-Cys-tetrahedral-intermediate (with previous peptide)Acyl-enzyme(Peptidyl-Cys-acyl group)Peptidyl-Cys-tetrahedral-intermediate
Typepeptide/proteinpeptide/proteinH2Opeptide/proteinpeptide/protein


ChEBI

15377





PubChem

962
22247451





                
1a2zAUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1a2zBUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1a2zCUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1a2zDUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1iofAUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1iofBUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1iofCUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1iofDUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1ioiAUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1ioiBUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1ioiCUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1ioiDUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1augAUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1augBUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1augCUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1augDUnboundUnbound UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P46107,PDB;1a2z
pdbCatalytic residuesMain-chain involved in catalysiscomment
           
1a2zAGLU  80;ARG  90;CYS 143;HIS 167
CYS 143
 
1a2zBGLU  80;ARG  90;CYS 143;HIS 167
CYS 143
 
1a2zCGLU  80;ARG  90;CYS 143;HIS 167
CYS 143
 
1a2zDGLU  80;ARG  90;CYS 143;HIS 167
CYS 143
 
1iofAGLU  79;ARG  89;CYS 142;HIS 166
CYS 142
 
1iofBGLU  79;ARG  89;CYS 142;HIS 166
CYS 142
 
1iofCGLU  79;ARG  89;CYS 142;HIS 166
CYS 142
 
1iofDGLU  79;ARG  89;CYS 142;HIS 166
CYS 142
 
1ioiAGLU  79;ARG  89;       ;HIS 166
       
mutant C142S
1ioiBGLU  79;ARG  89;       ;HIS 166
       
mutant C142S
1ioiCGLU  79;ARG  89;       ;HIS 166
       
mutant C142S
1ioiDGLU  79;ARG  89;       ;HIS 166
       
mutant C142S
1augAGLU  81;ARG  91;CYS 144;HIS 168
CYS 144
 
1augBGLU 291;ARG 301;CYS 354;HIS 378
CYS 354
 
1augCGLU 501;ARG 511;CYS 564;HIS 588
CYS 564
 
1augDGLU 711;ARG 721;CYS 774;HIS 798
CYS 774
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.240
[2]p.405
[3]p.111-112

references
[1]
CommentsX-ray crystallography (1.73 Angstroms)
PubMed ID10368293
JournalStructure Fold Des
Year1999
Volume7
Pages237-44
AuthorsSingleton M, Isupov M, Littlechild J
TitleX-ray structure of pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis.
Related PDB1a2z
[2]
CommentsX-ray crystallography (1.6 Angstroms)
Medline ID99216536
PubMed ID10196127
JournalStructure Fold Des
Year1999
Volume7
Pages399-411
AuthorsOdagaki Y, Hayashi A, Okada K, Hirotsu K, Kabashima T, Ito K, Yoshimoto T, Tsuru D, Sato M, Clardy J
TitleThe crystal structure of pyroglutamyl peptidase I from Bacillus amyloliquefaciens reveals a new structure for a cysteine protease.
Related PDB1aug
Related UniProtKBP46107
[3]
CommentsX-ray crystallography (wildtype;2.2/mutant;2.7 Angstroms)
PubMed ID11432786
JournalJ Biochem (Tokyo)
Year2001
Volume130
Pages107-18
AuthorsTanaka H, Chinami M, Mizushima T, Ogasahara K, Ota M, Tsukihara T, Yutani K
TitleX-ray crystalline structures of pyrrolidone carboxyl peptidase from a hyperthermophile, Pyrococcus furiosus, and its cys-free mutant.
Related PDB1iof,1ioi
[4]
CommentsX-ray crystallography, Site-directed mutagenesis
PubMed ID11359794
JournalJ Biol Chem
Year2001
Volume276
Pages18557-62
AuthorsIto K, Inoue T, Takahashi T, Huang HS, Esumi T, Hatakeyama S, Tanaka N, Nakamura KT, Yoshimoto T
TitleThe mechanism of aubstrate eecognition of pyroglutamyl-peptidase I from Bacillus amyloliquefaciens as determined by X-ray crystallography and site-directed mutagenesis.

comments
The papers [1],[2] & [3] reported on the catalytic triad Cys-His-Glu, suggesting that this enzyme belongs to a cysteine protease family. However, the mutation of the catalytic nucleophilic residue, Cys, into Ser, retained the catalytic activity [1].
According to the literature [2], the oxyanion hole seems to be composed of the mainchain amide of Cys144(PDB;1aug) and sidechain of Arg91.

createdupdated
2002-09-272012-10-22


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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.