DB code: D00189

RLCP classification 1.13.30000.10 : Hydrolysis
CATH domain 3.40.50.1820 : Rossmann fold Catalytic domain
1.10.287.410 : Helix Hairpins
E.C. 3.4.16.5
CSA 1ysc
M-CSA 1ysc
MACiE

CATH domain Related DB codes (homologues)
3.40.50.1820 : Rossmann fold S00544 S00344 S00517 S00525 S00526 S00720 S00723 S00724 S00725 S00919 S00057 S00374 S00345 S00347 S00348 S00346 S00350 S00352 S00353 S00355 S00356 S00358 D00210 D00539 T00253

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq MEROPS Pfam
P00729 Carboxypeptidase Y
EC 3.4.16.5
Carboxypeptidase YSCY
NP_014026.1 (Protein)
NM_001182806.1 (DNA/RNA sequence)
S10.001 (Serine)
PF05388 (Carbpep_Y_N)
PF00450 (Peptidase_S10)
[Graphical View]

KEGG enzyme name
carboxypeptidase C
carboxypeptidase Y
serine carboxypeptidase I
cathepsin A
lysosomal protective protein
deamidase
lysosomal carboxypeptidase A
phaseolin

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00729 CBPY_YEAST Release of a C-terminal amino acid with broad specificity. Vacuole. Note=Lysosome-like vacuoles.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00012 C00001 C00012 I00087 I00085 I00086
E.C.
Compound Peptide H2O Peptide Peptidyl-tetrahedral intermediate Acyl-enzyme Tetrahedral intermediate
Type peptide/protein H2O peptide/protein
ChEBI 15377
PubChem 962
22247451
1cpyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1yscA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1cpyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1yscA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1cpyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 146;ASP 338;HIS 397
1yscA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 146;ASP 338;HIS 397
1cpyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1yscA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
p.11116
[4]
Fig.8

References
[1]
Resource
Comments
Medline ID
PubMed ID 1459131
Journal Eur J Biochem
Year 1992
Volume 210
Pages 467-73
Authors Christensen U, Drohse HB, Molgaard L
Title Mechanism of carboxypeptidase-Y-catalysed peptide semisynthesis.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-ray crystallography (2.8 Angstroms)
Medline ID
PubMed ID 7727362
Journal Biochemistry
Year 1994
Volume 33
Pages 11106-20
Authors Endrizzi JA, Breddam K, Remington SJ
Title 2.8-A structure of yeast serine carboxypeptidase.
Related PDB 1cpy 1ysc
Related UniProtKB P00729
[3]
Resource
Comments catalysis
Medline ID
PubMed ID
Journal J Am Chem Soc
Year 1995
Volume 117
Pages 5944
Authors Sorensen SB, Raaschou-Nielsen M, Mortensen UH, Remington SJ, Breddam K
Title Site-directed mutagenesis on (serine) carboxypeptidase y from yeast. The significance of thr 60 and met 398 in hydrolysis and aminolysis reactions.
Related PDB 1cpy
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8679540
Journal Biochemistry
Year 1996
Volume 35
Pages 7131-41
Authors Stennicke HR, Mortensen UH, Breddam K
Title Studies on the hydrolytic properties of (serine) carboxypeptidase Y.
Related PDB
Related UniProtKB
[5]
Resource
Comments catalysis (ligand specificity)
Medline ID
PubMed ID 9336845
Journal Protein Sci
Year 1997
Volume 6
Pages 2227-32
Authors Sorensen SB, Breddam K
Title The specificity of carboxypeptidase Y may be altered by changing the hydrophobicity of the S'1 binding pocket.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 10021925
Journal Bioorg Med Chem Lett
Year 1999
Volume 9
Pages 187-92
Authors Mock WL, Xu D
Title Catalytic activity of carboxypeptidase B and of carboxypeptidase Y with anisylazoformyl substrates.
Related PDB
Related UniProtKB
[7]
Resource
Comments conformational stability
Medline ID
PubMed ID 10336632
Journal Eur J Biochem
Year 1999
Volume 262
Pages 475-83
Authors Dumoulin M, Ueno H, Hayashi R, Balny C
Title Contribution of the carbohydrate moiety to conformational stability of the carboxypeptidase Y high pressure study.
Related PDB
Related UniProtKB
[8]
Resource
Comments catalysis (mutation analysis)
Medline ID
PubMed ID 10427689
Journal Biosci Biotechnol Biochem
Year 1999
Volume 63
Pages 1045-50
Authors Shimizu H, Ueno H, Hayashi R
Title Role of carbohydrate moiety in carboxypeptidase Y: structural study of mutant enzyme lacking carbohydrate moiety.
Related PDB
Related UniProtKB

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.

Created Updated
2003-01-27 2011-02-16