P00729 (CBPY_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Carboxypeptidase Y
Short name=cpY
EC=3.4.16.5

Alternative name(s):
Carboxypeptidase YSCY

Gene names

Name:	PRC1
Ordered Locus Names:	YMR297W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	532 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in degradation of small peptides. Digests preferentially peptides containing an aliphatic or hydrophobic residue in P1' position, as well as methionine, leucine or phenylalanine in P1 position of ester substrate.
Catalytic activity	Release of a C-terminal amino acid with broad specificity.
Enzyme regulation	Inhibited by ZPCK.
Subcellular location	Vacuole. Note: Lysosome-like vacuoles.
Post-translational modification	Enters the endoplasmic reticulum as an inactive zymogen and is modified by four N-linked core oligosaccharides, giving rise to a precursor known as P1 (67 kDa). As P1 transits through the Golgi, extension of its core oligosaccharides leads to the Golgi-modified P2 precursor (69 kDa). P2 is sorted away from secretory proteins at or beyond a late Golgi compartment and is subsequently delivered to the vacuole via a prevacuolar endosome-like compartment. Upon arrival in the vacuole, the N-terminal prosegment of P2 is cleaved to yield the enzymatically active mature vacuolar form of CPY (61 kDa).
Miscellaneous	Present with 44000 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the peptidase S10 family.

Ontologies

Keywords
Cellular component	Vacuole
Domain	Signal
Molecular function	Carboxypeptidase Hydrolase Protease
PTM	Disulfide bond Glycoprotein Zymogen
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	phytochelatin biosynthetic process Inferred from direct assay PubMed 17408619. Source: SGD proteolysis Inferred from electronic annotation. Source: UniProtKB-KW vacuolar protein catabolic process Traceable author statement PubMed 8789256. Source: SGD
Cellular_component	endoplasmic reticulum Inferred from direct assay PubMed 11914276. Source: SGD fungal-type vacuole lumen Traceable author statement PubMed 9529893. Source: SGD
Molecular_function	serine-type carboxypeptidase activity Inferred from direct assay PubMed 8679540. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
HRD1	Q08109	2	EBI-4153,EBI-37613
HRD3	Q05787	2	EBI-4153,EBI-31647
YOS9	Q99220	2	EBI-4153,EBI-34938

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 20

20

Potential

Propeptide

21 – 111

91

PRO_0000004293

Chain

112 – 532

421

Carboxypeptidase Y

PRO_0000004294

Regions

Motif

24 – 27

4

Vacuolar targeting signal

Sites

Active site

257

1

Ref.5 Ref.9

Active site

449

1

By similarity

Active site

508

1

Ref.6

Binding site

452

1

Substrate

Binding site

509

1

Substrate

Amino acid modifications

Glycosylation

124

1

N-linked (GlcNAc...)

Glycosylation

198

1

N-linked (GlcNAc...)

Glycosylation

279

1

N-linked (GlcNAc...)

Glycosylation

479

1

N-linked (GlcNAc...)

Disulfide bond

167 ↔ 409

Disulfide bond

304 ↔ 318

Disulfide bond

328 ↔ 351

Disulfide bond

335 ↔ 344

Disulfide bond

373 ↔ 379

Experimental info

Mutagenesis

508

1

H → A or R: Inactivates enzyme.

Sequence conflict

260 – 261

2

GH → HG AA sequence Ref.4

Sequence conflict

389

1

Y → E AA sequence Ref.4

Sequence conflict

529

1

G → D AA sequence Ref.4

Secondary structure

1

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532

Helix Strand Turn

Details...

Helix

116 – 118

3

Beta strand

119 – 121

3

Beta strand

129 – 134

6

Turn

135 – 138

4

Beta strand

139 – 146

8

Turn

152 – 154

3

Beta strand

157 – 161

5

Turn

164 – 166

3

Helix

170 – 173

4

Turn

174 – 177

4

Beta strand

178 – 183

6

Turn

184 – 186

3

Beta strand

187 – 190

4

Helix

195 – 198

4

Beta strand

199 – 202

4

Beta strand

214 – 217

4

Helix

224 – 240

17

Helix

242 – 244

3

Turn

245 – 248

4

Beta strand

251 – 256

6

Helix

259 – 270

12

Beta strand

282 – 287

6

Helix

292 – 295

4

Helix

296 – 298

3

Helix

299 – 303

5

Beta strand

307 – 309

3

Helix

315 – 338

24

Helix

341 – 355

15

Helix

357 – 362

6

Beta strand

368 – 371

4

Beta strand

375 – 377

3

Helix

382 – 391

10

Helix

393 – 398

6

Beta strand

403 – 405

3

Helix

411 – 418

8

Turn

419 – 421

3

Helix

422 – 424

3

Helix

428 – 436

9

Beta strand

441 – 446

6

Helix

454 – 463

10

Helix

469 – 474

6

Beta strand

478 – 481

4

Turn

483 – 485

3

Beta strand

487 – 492

6

Beta strand

498 – 503

6

Helix

510 – 513

4

Helix

515 – 526

12

Turn

527 – 529

3

Sequences

	Sequence		Length	Mass (Da)
	P00729 [UniParc]. Last modified November 1, 1988. Version 1. Checksum: 7227F3489CBDD952	FASTA	532	59,802
	10 20 30 40 50 60 MKAFTSLLCG LGLSTTLAKA ISLQRPLGLD KDVLLQAAEK FGLDLDLDHL LKELDSNVLD 70 80 90 100 110 120 AWAQIEHLYP NQVMSLETST KPKFPEAIKT KKDWDFVVKN DAIENYQLRV NKIKDPKILG 130 140 150 160 170 180 IDPNVTQYTG YLDVEDEDKH FFFWTFESRN DPAKDPVILW LNGGPGCSSL TGLFFELGPS 190 200 210 220 230 240 SIGPDLKPIG NPYSWNSNAT VIFLDQPVNV GFSYSGSSGV SNTVAAGKDV YNFLELFFDQ 250 260 270 280 290 300 FPEYVNKGQD FHIAGESYAG HYIPVFASEI LSHKDRNFNL TSVLIGNGLT DPLTQYNYYE 310 320 330 340 350 360 PMACGEGGEP SVLPSEECSA MEDSLERCLG LIESCYDSQS VWSCVPATIY CNNAQLAPYQ 370 380 390 400 410 420 RTGRNVYDIR KDCEGGNLCY PTLQDIDDYL NQDYVKEAVG AEVDHYESCN FDINRNFLFA 430 440 450 460 470 480 GDWMKPYHTA VTDLLNQDLP ILVYAGDKDF ICNWLGNKAW TDVLPWKYDE EFASQKVRNW 490 500 510 520 530 TASITDEVAG EVKSYKHFTY LRVFNGGHMV PFDVPENALS MVNEWIHGGF SL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Protein sorting in yeast: the localization determinant of yeast vacuolar carboxypeptidase Y resides in the propeptide." Valls L.A., Hunter C.P., Rothman J.H., Stevens T.H. Cell 48:887-897(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII." Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T., Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P. , Skelton J., Walsh S.V., Whitehead S., Barrell B.G. Nature 387:90-93(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Amino acid sequence of carboxypeptidase Y. II. Peptides from enzymatic cleavages." Svendsen I., Martin B.M., Viswanatha T., Johansen J.T. Carlsberg Res. Commun. 47:15-27(1982) Cited for: PROTEIN SEQUENCE OF 112-532.
[5]	"Identification of methionyl and cysteinyl residues in the substrate binding site of carboxypeptidase Y." Breddam K., Svendsen I. Carlsberg Res. Commun. 49:639-645(1984) Cited for: SEQUENCE REVISION, ACTIVE SITE SER-257.
[6]	"Inactivation of carboxypeptidase Y by mutational removal of the putative essential histidyl residue." Bech L.M., Breddam K. Carlsberg Res. Commun. 54:165-171(1989) [PubMed] [Europe PMC] [Abstract] Cited for: ACTIVE SITE HIS-508.
[7]	"Site-directed mutagenesis on (serine) carboxypeptidase Y. A hydrogen bond network stabilizes the transition state by interaction with the C-terminal carboxylate group of the substrate." Mortensen U.H., Remington S.J., Breddam K. Biochemistry 33:508-517(1994) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS.
[8]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[9]	"2.8-A structure of yeast serine carboxypeptidase." Endrizzi J.A., Breddam K., Remington S.J. Biochemistry 33:11106-11120(1994) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
+	Additional computationally mapped references.

Web resources

Worthington enzyme manual

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M15482 Genomic DNA. Translation: AAA34902.1.
X80836 Genomic DNA. Translation: CAA56806.1.
BK006946 Genomic DNA. Translation: DAA10198.1.

PIR

CPBYY. A26597.

RefSeq

NP_014026.1. NM_001182806.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CPY	X-ray	2.60	A	112-532	[»]
1WPX	X-ray	2.70	A	112-532	[»]
1YSC	X-ray	2.80	A	112-532	[»]

ProteinModelPortal

P00729.

SMR

P00729. Positions 112-532.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2394N.

IntAct

P00729. 14 interactions.

MINT

MINT-1956986.

STRING

4932.YMR297W.

Protein family/group databases

Allergome

8267. Sac c Carboxypeptidase Y.

MEROPS

S10.001.

Proteomic databases

PaxDb

P00729.

PeptideAtlas

P00729.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YMR297W; YMR297W; YMR297W.

GeneID

855343.

KEGG

sce:YMR297W.

Organism-specific databases

CYGD

YMR297w.

SGD

S000004912. PRC1.

Phylogenomic databases

eggNOG

COG2939.

GeneTree

ENSGT00560000077221.

HOGENOM

HOG000198296.

KO

K13289.

OMA

ECSAMED.

OrthoDB

EOG4Z9252.

Enzyme and pathway databases

BioCyc

YEAST:YMR297W-MONOMER.

Gene expression databases

Genevestigator

P00729.

GermOnline

YMR297W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR001563. Peptidase_S10.
IPR018202. Peptidase_S10_AS.
IPR008442. Propeptide_carboxypepY.
[Graphical view]

PANTHER

PTHR11802. PTHR11802. 1 hit.

Pfam

PF05388. Carbpep_Y_N. 1 hit.
PF00450. Peptidase_S10. 1 hit.
[Graphical view]

PRINTS

PR00724. CRBOXYPTASEC.

PROSITE

PS00560. CARBOXYPEPT_SER_HIS. 1 hit.
PS00131. CARBOXYPEPT_SER_SER. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P00729.

NextBio

979085.

Entry information

Entry name

CBPY_YEAST

Accession

Primary (citable) accession number: P00729
Secondary accession number(s): D6W0C4

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	November 1, 1988
Last modified:	May 29, 2013
This is version 154 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program