Reviewed, UniProtKB/Swiss-Prot P32379 (PSA5_YEAST)

Names and origin

Protein names

Recommended name:
    Proteasome component PUP2
    EC=3.4.25.1
Alternative name(s):
    Macropain subunit PUP2
    Proteinase YSCE subunit PUP2
    Multicatalytic endopeptidase complex subunit PUP2

Gene names

Name:	PUP2
Synonyms:	DOA5
Ordered Locus Names:	YGR253C
ORF Names:	G9155

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	260 AA.
Sequence status	Complete.
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.6
Sequence similarities	Belongs to the peptidase T1A family.

Ontologies

Keywords
Cellular component	Cytoplasm Nucleus Proteasome
Molecular function	Hydrolase Protease Threonine protease
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	ascospore formation Traceable author statement. Source: SGD response to stress Traceable author statement. 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.11 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
ARO8	P53090	1	EBI-13971,EBI-2042933
CYS4	P32582	1	EBI-13971,EBI-4167
GLN1	P32288	1	EBI-13971,EBI-7665
IPP1	P00817	1	EBI-13971,EBI-9338
PRE10	P21242	1	EBI-13971,EBI-13963
VAS1	P07806-1	1	EBI-13971,EBI-1009942

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 260

260

Proteasome component PUP2

PRO_0000124129

Amino acid modifications

Modified residue

16

1

Phosphoserine Ref.7

Modified residue

35

1

Phosphoserine Ref.10

Modified residue

55

1

Phosphothreonine Ref.8 Ref.9

Modified residue

56

1

Phosphoserine Ref.7 Ref.10 Ref.8 Ref.9

Modified residue

87

1

Phosphoserine Ref.10

Modified residue

251

1

Phosphoserine Ref.10 Ref.8

Modified residue

260

1

Phosphoserine Ref.10

Experimental info

Mutagenesis

49

1

G → D in DOA5-1; slight decrease in activity. Ref.2

Sequence conflict

192

1

T → S in CAA46111. Ref.1

Secondary structure

1

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260

Helix Strand Turn

Details...

Helix

22 – 31

10

Beta strand

37 – 41

5

Beta strand

46 – 51

6

Helix

61 – 63

3

Beta strand

67 – 71

5

Beta strand

74 – 81

8

Helix

82 – 84

3

Helix

85 – 103

19

Helix

109 – 117

9

Turn

118 – 121

4

Beta strand

124 – 126

3

Beta strand

134 – 136

3

Beta strand

139 – 148

10

Turn

149 – 151

3

Beta strand

152 – 158

7

Beta strand

164 – 173

10

Helix

176 – 186

11

Helix

193 – 207

15

Beta strand

216 – 223

8

Turn

224 – 226

3

Beta strand

227 – 230

4

Helix

233 – 247

15

Sequences

	Sequence		Length	Mass (Da)
	P32379-1 [UniParc]. Last modified October 1, 1996. Version 2. Checksum: E8EDEB212BF4EC6E	FASTA	260	28,617
	10 20 30 40 50 60 MFLTRSEYDR GVSTFSPEGR LFQVEYSLEA IKLGSTAIGI ATKEGVVLGV EKRATSPLLE 70 80 90 100 110 120 SDSIEKIVEI DRHIGCAMSG LTADARSMIE HARTAAVTHN LYYDEDINVE SLTQSVCDLA 130 140 150 160 170 180 LRFGEGASGE ERLMSRPFGV ALLIAGHDAD DGYQLFHAEP SGTFYRYNAK AIGSGSEGAQ 190 200 210 220 230 240 AELLNEWHSS LTLKEAELLV LKILKQVMEE KLDENNAQLS CITKQDGFKI YDNEKTAELI 250 260 KELKEKEAAE SPEEADVEMS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning of an essential yeast gene encoding a proteasomal subunit." Georgatsou E., Georgakopoulos T., Thireos G. FEBS Lett. 299:39-43(1992) [PubMed: 1544471] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Biogenesis, structure and function of the yeast 20S proteasome." Chen P., Hochstrasser M. EMBO J. 14:2620-2630(1995) [PubMed: 7781614] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF GLY-49.
[3]	"Sequence analysis of a 10.5 kb DNA fragment from the yeast chromosome VII reveals the presence of three new open reading frames and of a tRNAThr gene." Mazzoni C., Ruzzi M., Rinaldi T., Solinas F., Montebove F., Frontali L. Yeast 13:369-372(1997) [PubMed: 9133741] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"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 204508 / S288c.
[5]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	"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].
[7]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed: 15665377] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-16 AND SER-56, MASS SPECTROMETRY.
[8]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-55; SER-56 AND SER-251, MASS SPECTROMETRY.
[9]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-55 AND SER-56, MASS SPECTROMETRY.
[10]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-35; SER-56; SER-87; SER-251 AND SER-260, MASS SPECTROMETRY.
[11]	"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 9-250 OF COMPLEX WITH THE 20S PROTEASOME.
[12]	"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).
[13]	"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 1-250 OF COMPLEX WITH THE 20S PROTEASOME.
[14]	"Crystal structure of the 20 S proteasome:TMC-95A complex: a non-covalent proteasome inhibitor." Groll M., Koguchi Y., Huber R., Kohno J. J. Mol. Biol. 311:543-548(2001) [PubMed: 11493007] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 9-250 OF COMPLEX WITH THE 20S PROTEASOME.
[15]	"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 9-250 OF COMPLEX WITH THE 20S PROTEASOME.
[16]	"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 9-250 OF COMPLEX WITH THE 20S PROTEASOME.
[17]	"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 9-250 OF COMPLEX WITH THE 20S PROTEASOME.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X64918 Genomic DNA. Translation: CAA46111.1.
X99228 Genomic DNA. Translation: CAA67615.1.
Z73038 Genomic DNA. Translation: CAA97282.1.
AY558511 Genomic DNA. Translation: AAS56837.1.

PIR

S64585.

RefSeq

NP_011769.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FNT	X-ray	3.20	E/S	1-260	[»]
1G0U	X-ray	2.40	D/R	1-250	[»]
1G65	X-ray	2.25	D/R	9-250	[»]
1JD2	X-ray	3.00	D/Y	9-250	[»]
1RYP	X-ray	1.90	E/S	9-250	[»]
1Z7Q	X-ray	3.22	E/S	1-260	[»]
2F16	X-ray	2.80	D/R	9-250	[»]
2FAK	X-ray	2.80	D/R	9-250	[»]
2GPL	X-ray	2.81	D/R	9-250	[»]
2Z5C	X-ray	2.90	C/F	1-260	[»]
2ZCY	X-ray	2.90	D/R	1-260	[»]
3BDM	X-ray	2.70	D/R	1-260	[»]
3D29	X-ray	2.60	D/R	9-250	[»]
3DY3	X-ray	2.81	D/R	9-250	[»]
3DY4	X-ray	2.80	D/R	9-250	[»]
3E47	X-ray	3.00	D/R	9-250	[»]
3GPJ	X-ray	2.70	D/R	9-250	[»]
3GPT	X-ray	2.41	D/R	9-250	[»]
3GPW	X-ray	2.50	D/R	9-250	[»]
3HYE	X-ray	2.50	D/R	9-250	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1193N.

IntAct

P32379. 16 interactions.

STRING

P32379.

Protein family/group databases

MEROPS

T01.975.

Proteomic databases

PeptideAtlas

P32379.

PRIDE

P32379.

Genome annotation databases

Ensembl

YGR253C; YGR253C; YGR253C; Saccharomyces cerevisiae. [Genome view]

GeneID

853168.

KEGG

sce:YGR253C.

NMPDR

fig|4932.3.peg.2898.

Organism-specific databases

CYGD

YGR253c.

SGD

S000003485. PUP2.

Phylogenomic databases

eggNOG

fuNOG04476.

HOGENOM

HBG499923.

OMA

LMSRPFG.

OrthoDB

EOG9VX3NQ.

PhylomeDB

P32379.

Enzyme and pathway databases

BRENDA

3.4.25.1. 250.

Gene expression databases

ArrayExpress

P32379.

Genevestigator

P32379.

GermOnline

YGR253C. 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. 1 hit.
PS51475. PROTEASOME_A_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

973285.

Entry information

Entry name

PSA5_YEAST

Accession

Primary (citable) accession number: P32379

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	October 1, 1996
Last modified:	February 9, 2010
This is version 111 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)