Reviewed, UniProtKB/Swiss-Prot P23638 (PSA4_YEAST)

Names and origin

Protein names

Recommended name:
    Proteasome component Y13
    EC=3.4.25.1
Alternative name(s):
    Macropain subunit Y13
    Proteinase YSCE subunit 13
    Multicatalytic endopeptidase complex subunit Y13

Gene names

Name:	PRE9
Synonyms:	PRS5
Ordered Locus Names:	YGR135W

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	258 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity.
Catalytic activity	Cleavage of peptide bonds with very broad specificity.
Subunit structure	The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel.
Subcellular location	Cytoplasm. Nucleus.
Miscellaneous	Present with 17100 molecules/cell in log phase SD medium. Ref.3
Sequence similarities	Belongs to the peptidase T1A family.

Ontologies

Keywords
Cellular component	Cytoplasm Nucleus Proteasome
Molecular function	Hydrolase Protease Threonine protease
PTM	Isopeptide bond Ubl conjugation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	filamentous growth Inferred from mutant phenotype. Source: SGD ubiquitin-dependent protein catabolic process Traceable author statement. Source: SGD
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell proteasome core complex, alpha-subunit complex Ref.5 Inferred from physical interaction. Source: SGD proteasome storage granule Inferred from direct assay. Source: SGD
Molecular function	protein binding Inferred from physical interaction. Source: IntAct threonine-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PRE10	P21242	1	EBI-13967,EBI-13963
PRE8	P23639	1	EBI-13967,EBI-13959

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 258

258

Proteasome component Y13

PRO_0000124116

Amino acid modifications

Cross-link

199

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4

Secondary structure

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258

Helix Strand Turn

Details...

Helix

4 – 6

3

Helix

20 – 29

10

Beta strand

35 – 40

6

Beta strand

43 – 49

7

Beta strand

55 – 57

3

Beta strand

64 – 79

16

Helix

81 – 102

22

Helix

108 – 124

17

Beta strand

125 – 127

3

Beta strand

133 – 141

9

Turn

142 – 144

3

Beta strand

145 – 151

7

Beta strand

157 – 166

10

Helix

169 – 179

11

Helix

186 – 200

15

Beta strand

202 – 205

4

Helix

208 – 210

3

Beta strand

211 – 217

7

Beta strand

220 – 224

5

Beta strand

226 – 229

4

Helix

232 – 241

10

Sequences

	Sequence		Length	Mass (Da)
	P23638-1 [UniParc]. Last modified November 1, 1991. Version 1. Checksum: B43BB05233A01A9E	FASTA	258	28,714
	10 20 30 40 50 60 MGSRRYDSRT TIFSPEGRLY QVEYALESIS HAGTAIGIMA SDGIVLAAER KVTSTLLEQD 70 80 90 100 110 120 TSTEKLYKLN DKIAVAVAGL TADAEILINT ARIHAQNYLK TYNEDIPVEI LVRRLSDIKQ 130 140 150 160 170 180 GYTQHGGLRP FGVSFIYAGY DDRYGYQLYT SNPSGNYTGW KAISVGANTS AAQTLLQMDY 190 200 210 220 230 240 KDDMKVDDAI ELALKTLSKT TDSSALTYDR LEFATIRKGA NDGEVYQKIF KPQEIKDILV 250 KTGITKKDED EEADEDMK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning and functional analysis of three subunits of yeast proteasome." Emori Y., Tsukahara T., Kawasaki H., Ishiura S., Sugita H., Suzuki K. Mol. Cell. Biol. 11:344-353(1991) [PubMed: 1898763] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 73-92; 120-139 AND 200-236. Strain: ATCC 26786 / X2180-1A.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII." Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E. , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K. Nature 387:81-84(1997) [PubMed: 9169869] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[4]	"A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery." Hitchcock A.L., Auld K., Gygi S.P., Silver P.A. Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003) [PubMed: 14557538] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-199, MASS SPECTROMETRY.
[5]	"Structure of 20S proteasome from yeast at 2.4-A resolution." Groll M., Ditzel L., Loewe J., Stock D., Bochtler M., Bartunik H.D., Huber R. Nature 386:463-471(1997) [PubMed: 9087403] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 2-245 OF COMPLEX WITH THE 20S PROTEASOME.
[6]	"Structural basis for the activation of 20S proteasomes by 11S regulators." Whitby F.G., Masters E.I., Kramer L., Knowlton J.R., Yao Y., Wang C.C., Hill C.P. Nature 408:115-120(2000) [PubMed: 11081519] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF 1-245 OF COMPLEX WITH THE 20S PROTEASOME AND A 11S REGULATORY COMPLEX.
[7]	"A gated channel into the proteasome core particle." Groll M., Bajorek M., Koehler A., Moroder L., Rubin D.M., Huber R., Glickman M.H., Finley D. Nat. Struct. Biol. 7:1062-1067(2000) [PubMed: 11062564] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 1-245 OF COMPLEX WITH THE 20S PROTEASOME.
[8]	"TMC-95-based inhibitor design provides evidence for the catalytic versatility of the proteasome." Groll M., Goetz M., Kaiser M., Weyher E., Moroder L. Chem. Biol. 13:607-614(2006) [PubMed: 16793518] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.81 ANGSTROMS) OF 2-245 OF COMPLEX WITH THE 20S PROTEASOME AND A TMC-95-BASED INHIBITOR.
[9]	"Crystal structures of salinosporamide A (NPI-0052) and B (NPI-0047) in complex with the 20S proteasome reveal important consequences of beta-lactone ring opening and a mechanism for irreversible binding." Groll M., Huber R., Potts B.C.M. J. Am. Chem. Soc. 128:5136-5141(2006) [PubMed: 16608349] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 2-245 OF COMPLEX WITH THE 20S PROTEASOME AND SALINOSPORAMIDE.
[10]	"Crystal structure of the boronic acid-based proteasome inhibitor bortezomib in complex with the yeast 20S proteasome." Groll M., Berkers C.R., Ploegh H.L., Ovaa H. Structure 14:451-456(2006) [PubMed: 16531229] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 2-245 OF COMPLEX WITH THE 20S PROTEASOME AND BORTEZOMIB.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M63851 Genomic DNA. Translation: AAA34907.1.
X56730 Genomic DNA. Translation: CAA40054.1.
Z72920 Genomic DNA. Translation: CAA97148.1.

PIR

SNBYY3. S12940.

RefSeq

NP_011651.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FNT	X-ray	3.20	C/Q	1-245	[»]
1G0U	X-ray	2.40	B/P	1-245	[»]
1G65	X-ray	2.25	B/P	2-245	[»]
1JD2	X-ray	3.00	B/W	2-245	[»]
1RYP	X-ray	1.90	C/Q	2-245	[»]
1Z7Q	X-ray	3.22	C/Q	1-258	[»]
2F16	X-ray	2.80	B/P	2-245	[»]
2FAK	X-ray	2.80	B/P	2-245	[»]
2GPL	X-ray	2.81	B/P	2-245	[»]
2ZCY	X-ray	2.90	B/P	1-258	[»]
3BDM	X-ray	2.70	B/P	1-258	[»]
3D29	X-ray	2.60	B/P	2-245	[»]
3DY3	X-ray	2.81	B/P	2-245	[»]
3DY4	X-ray	2.80	B/P	2-245	[»]
3E47	X-ray	3.00	B/P	2-245	[»]
3GPJ	X-ray	2.70	B/P	2-245	[»]
3GPT	X-ray	2.41	B/P	2-245	[»]
3GPW	X-ray	2.50	B/P	2-245	[»]
3HYE	X-ray	2.50	B/P	2-245	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:2823N.

IntAct

P23638. 19 interactions.

STRING

P23638.

Protein family/group databases

MEROPS

T01.973.

Proteomic databases

PeptideAtlas

P23638.

PRIDE

P23638.

Genome annotation databases

Ensembl

YGR135W; YGR135W; YGR135W; Saccharomyces cerevisiae. [Genome view]

GeneID

853036.

GenomeReviews

Gene locus YGR135W in contig Y13135_GR.

KEGG

sce:YGR135W.

NMPDR

fig|4932.3.peg.2770.

Organism-specific databases

CYGD

YGR135w.

SGD

S000003367. PRE9.

Phylogenomic databases

HOGENOM

P23638.

OMA

MARRYDS.

Enzyme and pathway databases

BRENDA

3.4.25.1. 250.

Gene expression databases

ArrayExpress

P23638.

Genevestigator

P23638.

GermOnline

YGR135W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR000426. Proteasome_asu_CS.
IPR001353. Proteasome_sua/b.
[Graphical view]

Pfam

PF00227. Proteasome. 1 hit.
PF10584. Proteasome_A_N. 1 hit.
[Graphical view]

PROSITE

PS00388. PROTEASOME_A. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

972935.

Entry information

Entry name

PSA4_YEAST

Accession

Primary (citable) accession number: P23638

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1991
Last sequence update:	November 1, 1991
Last modified:	November 3, 2009
This is version 102 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)