EzCatDB: D00189
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DB codeD00189
RLCP classification1.13.30000.10 : Hydrolysis
CATH domainDomain 13.40.50.1820 : Rossmann foldCatalytic domain
Domain 21.10.287.410 : Helix Hairpins
E.C.3.4.16.5
CSA1ysc

CATH domainRelated DB codes (homologues)
3.40.50.1820 : Rossmann foldS00544,S00344,S00517,S00525,S00526,S00720,S00723,S00724,S00725,S00919,S00057,S00374,S00345,S00347,S00348,S00346,S00350,S00352,S00353,S00355,S00356,S00358,D00210,D00539,T00253

Enzyme Name
UniProtKBKEGG

P00729
Protein nameCarboxypeptidase Ycarboxypeptidase C
carboxypeptidase Y
serine carboxypeptidase I
cathepsin A
lysosomal protective protein
deamidase
lysosomal carboxypeptidase A
phaseolin
SynonymscpY
EC 3.4.16.5
Carboxypeptidase YSCY
RefSeqNP_014026.1 (Protein)
NM_001182806.1 (DNA/RNA sequence)
MEROPSS10.001 (Serine)
PfamPF05388 (Carbpep_Y_N)
PF00450 (Peptidase_S10)
[Graphical view]


UniProtKB:Accession NumberP00729
Entry nameCBPY_YEAST
ActivityRelease of a C-terminal amino acid with broad specificity.
Subunit
Subcellular locationVacuole. Note=Lysosome-like vacuoles.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00012C00001C00012I00087I00085I00086
CompoundPeptideH2OPeptidePeptidyl-tetrahedral intermediateAcyl-enzymeTetrahedral intermediate
Typepeptide/proteinH2Opeptide/protein


ChEBI
15377




PubChem
22247451
962




              
1cpyA01Unbound Unbound   
1yscA01Unbound Unbound   
1cpyA02Unbound Unbound   
1yscA02Unbound Unbound   

Active-site residues
pdbCatalytic residues
         
1cpyA01SER 146;ASP 338;HIS 397
1yscA01SER 146;ASP 338;HIS 397
1cpyA02 
1yscA02 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.11116
[4]Fig.8

references
[1]
PubMed ID1459131
JournalEur J Biochem
Year1992
Volume210
Pages467-73
AuthorsChristensen U, Drohse HB, Molgaard L
TitleMechanism of carboxypeptidase-Y-catalysed peptide semisynthesis.
[2]
CommentsX-ray crystallography (2.8 Angstroms)
PubMed ID7727362
JournalBiochemistry
Year1994
Volume33
Pages11106-20
AuthorsEndrizzi JA, Breddam K, Remington SJ
Title2.8-A structure of yeast serine carboxypeptidase.
Related PDB1cpy,1ysc
Related UniProtKBP00729
[3]
Commentscatalysis
JournalJ Am Chem Soc
Year1995
Volume117
Pages5944
AuthorsSorensen SB, Raaschou-Nielsen M, Mortensen UH, Remington SJ, Breddam K
TitleSite-directed mutagenesis on (serine) carboxypeptidase y from yeast. The significance of thr 60 and met 398 in hydrolysis and aminolysis reactions.
Related PDB1cpy
[4]
PubMed ID8679540
JournalBiochemistry
Year1996
Volume35
Pages7131-41
AuthorsStennicke HR, Mortensen UH, Breddam K
TitleStudies on the hydrolytic properties of (serine) carboxypeptidase Y.
[5]
Commentscatalysis (ligand specificity)
PubMed ID9336845
JournalProtein Sci
Year1997
Volume6
Pages2227-32
AuthorsSorensen SB, Breddam K
TitleThe specificity of carboxypeptidase Y may be altered by changing the hydrophobicity of the S'1 binding pocket.
[6]
PubMed ID10021925
JournalBioorg Med Chem Lett
Year1999
Volume9
Pages187-92
AuthorsMock WL, Xu D
TitleCatalytic activity of carboxypeptidase B and of carboxypeptidase Y with anisylazoformyl substrates.
[7]
Commentsconformational stability
PubMed ID10336632
JournalEur J Biochem
Year1999
Volume262
Pages475-83
AuthorsDumoulin M, Ueno H, Hayashi R, Balny C
TitleContribution of the carbohydrate moiety to conformational stability of the carboxypeptidase Y high pressure study.
[8]
Commentscatalysis (mutation analysis)
PubMed ID10427689
JournalBiosci Biotechnol Biochem
Year1999
Volume63
Pages1045-50
AuthorsShimizu H, Ueno H, Hayashi R
TitleRole of carbohydrate moiety in carboxypeptidase Y: structural study of mutant enzyme lacking carbohydrate moiety.

comments
This enzyme belongs to the peptidase family S10.
According to the literature [2], this enzyme contains a catalytic triad, Ser146/Asp338/His397 (PDB; 1cpy), which is similar to those of trypsine-like serine peptidases. In this enzyme, Ser146 acts as a nucleophile, and His397 acts as Acid/Base. The negatively charged tetrahedral intermediate during catalysis is stablized by the oxyanion hole composed of the backbone amides.

createdupdated
2003-01-272011-02-16
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 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 - )
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