P25043 (PSB2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Proteasome subunit beta type-2
EC=3.4.25.1

Alternative name(s):
Macropain subunit PUP1
Multicatalytic endopeptidase complex subunit PUP1
Proteasome component PUP1
Proteinase YSCE subunit PUP1

Gene names

Name:	PUP1
Ordered Locus Names:	YOR157C

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	261 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	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	The side chain of Thr-30 acts as nucleophile, and the N-terminal amino group acts as proton acceptor. Present with 11400 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the peptidase T1B family.

Ontologies

Keywords
Cellular component	Cytoplasm Nucleus Proteasome
Molecular function	Hydrolase Protease Threonine protease
PTM	Zymogen
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	proteasomal ubiquitin-dependent protein catabolic process Inferred from direct assay PubMed 11545745PubMed 19029916. Source: SGD proteasomal ubiquitin-independent protein catabolic process Inferred from direct assay PubMed 19162040. Source: SGD
Cellular_component	endoplasmic reticulum membrane Inferred by curator Ref.6. Source: SGD nucleus Inferred from direct assay PubMed 18504300. Source: SGD proteasome core complex, beta-subunit complex Inferred from direct assay Ref.6. Source: SGD proteasome storage granule Inferred from direct assay PubMed 18504300. Source: SGD
Molecular_function	endopeptidase activity Inferred from mutant phenotype PubMed 9207060PubMed 9312134. Source: SGD threonine-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PUP3	P25451	3	EBI-14009,EBI-13993

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Propeptide

1 – 29

29

Removed in mature form

PRO_0000026657

Chain

30 – 261

232

Proteasome subunit beta type-2

PRO_0000026658

Sites

Active site

30

1

Nucleophile Ref.6

Secondary structure

1

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261

Helix Strand Turn

Details...

Beta strand

32 – 37

6

Beta strand

40 – 45

6

Beta strand

49 – 51

3

Beta strand

54 – 59

6

Beta strand

63 – 67

5

Beta strand

70 – 76

7

Helix

78 – 99

22

Helix

105 – 118

14

Turn

119 – 121

3

Beta strand

125 – 133

9

Beta strand

136 – 142

7

Turn

144 – 146

3

Beta strand

148 – 150

3

Beta strand

152 – 157

6

Helix

160 – 170

11

Helix

177 – 194

18

Beta strand

202 – 208

7

Beta strand

213 – 220

8

Beta strand

241 – 246

6

Sequences

	Sequence		Length	Mass (Da)
	P25043 [UniParc]. Last modified May 1, 1992. Version 1. Checksum: 13A8F2B75584539A	FASTA	261	28,268
	10 20 30 40 50 60 MAGLSFDNYQ RNNFLAENSH TQPKATSTGT TIVGVKFNNG VVIAADTRST QGPIVADKNC 70 80 90 100 110 120 AKLHRISPKI WCAGAGTAAD TEAVTQLIGS NIELHSLYTS REPRVVSALQ MLKQHLFKYQ 130 140 150 160 170 180 GHIGAYLIVA GVDPTGSHLF SIHAHGSTDV GYYLSLGSGS LAAMAVLESH WKQDLTKEEA 190 200 210 220 230 240 IKLASDAIQA GIWNDLGSGS NVDVCVMEIG KDAEYLRNYL TPNVREEKQK SYKFPRGTTA 250 260 VLKESIVNIC DIQEEQVDIT A

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of PUP1 encoding a putative proteasome subunit in Saccharomyces cerevisiae." Haffter P., Fox T.D. Nucleic Acids Res. 19:5075-5075(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Analysis of a 35.6 kb region on the right arm of Saccharomyces cerevisiae chromosome XV." Bordonne R., Camasses A., Madania A., Poch O., Tarassov I.A., Winsor B., Martin R.P. Yeast 13:73-83(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: S288c / FY1678.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV." Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K. Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: S288c / FY1678.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"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].
[6]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 30-251 OF COMPLEX WITH THE 20S PROTEASOME, PROTEOLYTIC PROCESSING, ACTIVE SITE.
[7]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF 30-261 OF COMPLEX WITH THE 20S PROTEASOME AND A 11S REGULATORY COMPLEX.
[8]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF COMPLEX WITH THE 20S PROTEASOME.
[9]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.81 ANGSTROMS) OF 30-251 OF COMPLEX WITH THE 20S PROTEASOME AND A TMC-95-BASED INHIBITOR.
[10]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 30-251 OF COMPLEX WITH THE 20S PROTEASOME AND SALINOSPORAMIDE.
[11]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 30-251 OF COMPLEX WITH THE 20S PROTEASOME AND BORTEZOMIB.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X61189 Genomic DNA. Translation: CAA43492.1.
U55020 Genomic DNA. Translation: AAC49643.1.
Z75065 Genomic DNA. Translation: CAA99363.1.
BK006948 Genomic DNA. Translation: DAA10930.1.

PIR

S26996.

RefSeq

NP_014800.3. NM_001183576.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FNT	X-ray	3.20	I/W	30-261	[»]
1G0U	X-ray	2.40	H/V	30-251	[»]
1G65	X-ray	2.25	H/V	30-251	[»]
1JD2	X-ray	3.00	H/O	30-251	[»]
1RYP	X-ray	1.90	I/W	30-251	[»]
1VSY	X-ray	3.00	I/W	30-251	[»]
1Z7Q	X-ray	3.22	I/W	30-251	[»]
2F16	X-ray	2.80	H/V	30-251	[»]
2FAK	X-ray	2.80	H/V	30-251	[»]
2GPL	X-ray	2.81	H/V	30-251	[»]
2ZCY	X-ray	2.90	H/V	30-261	[»]
3BDM	X-ray	2.70	H/V	30-261	[»]
3D29	X-ray	2.60	H/V	30-251	[»]
3DY3	X-ray	2.81	H/V	30-251	[»]
3DY4	X-ray	2.80	H/V	30-251	[»]
3E47	X-ray	3.00	H/V	30-251	[»]
3GPJ	X-ray	2.70	H/V	30-251	[»]
3GPT	X-ray	2.41	H/V	30-251	[»]
3GPW	X-ray	2.50	H/V	30-251	[»]
3HYE	X-ray	2.50	H/V	30-251	[»]
3L5Q	X-ray	3.00	M/Y	30-251	[»]
3MG0	X-ray	2.68	H/V	30-251	[»]
3MG4	X-ray	3.11	H/V	30-251	[»]
3MG6	X-ray	2.60	H/V	30-251	[»]
3MG7	X-ray	2.78	H/V	30-251	[»]
3MG8	X-ray	2.59	H/V	30-251	[»]
3NZJ	X-ray	2.40	H/V	1-261	[»]
3NZW	X-ray	2.50	H/V	1-261	[»]
3NZX	X-ray	2.70	H/V	1-261	[»]
3OEU	X-ray	2.60	H/V	30-251	[»]
3OEV	X-ray	2.85	H/V	30-251	[»]
3OKJ	X-ray	2.70	H/V	30-251	[»]
3SDI	X-ray	2.65	H/V	30-251	[»]
3SDK	X-ray	2.70	H/V	30-251	[»]
3SHJ	X-ray	2.80	H/V	30-251	[»]
3TDD	X-ray	2.70	H/V	30-251	[»]
3UN4	X-ray	3.40	H/V	30-261	[»]
3UN8	X-ray	2.70	H/V	30-261	[»]
4B4T	electron microscopy	7.40	2	1-261	[»]
4FZC	X-ray	2.80	H/V	30-251	[»]
4FZG	X-ray	3.00	H/V	30-251	[»]
4G4S	X-ray	2.49	I	30-261	[»]
4GK7	X-ray	2.80	H/V	30-251	[»]
4INR	X-ray	2.70	H/V	30-261	[»]
4INT	X-ray	2.90	H/V	30-261	[»]
4INU	X-ray	3.10	H/V	30-261	[»]

ProteinModelPortal

P25043.

SMR

P25043. Positions 30-251.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2818N.

IntAct

P25043. 8 interactions.

MINT

MINT-498378.

STRING

4932.YOR157C.

Protein family/group databases

MEROPS

T01.011.

Proteomic databases

PaxDb

P25043.

PeptideAtlas

P25043.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOR157C; YOR157C; YOR157C.

GeneID

854328.

KEGG

sce:YOR157C.
sce:YOR159C.

Organism-specific databases

CYGD

YOR157c.

SGD

S000005683. PUP1.

Phylogenomic databases

eggNOG

COG0638.

GeneTree

ENSGT00510000046533.

HOGENOM

HOG000182856.

KO

K02739.
K11097.

OMA

GTTIVGC.

OrthoDB

EOG4V46HP.

Gene expression databases

Genevestigator

P25043.

GermOnline

YOR157C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR000243. Pept_T1A_subB.
IPR024689. Proteasome_bsu_C.
IPR016050. Proteasome_bsu_CS.
IPR001353. Proteasome_sua/b.
IPR023333. Proteasome_suB-type.
[Graphical view]

Pfam

PF12465. Pr_beta_C. 1 hit.
PF00227. Proteasome. 1 hit.
[Graphical view]

PRINTS

PR00141. PROTEASOME.

PROSITE

PS00854. PROTEASOME_B_1. 1 hit.
PS51476. PROTEASOME_B_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P25043.

NextBio

976378.

Entry information

Entry name

PSB2_YEAST

Accession

Primary (citable) accession number: P25043
Secondary accession number(s): D6W2L4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	May 1, 1992
Last modified:	April 3, 2013
This is version 135 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program