P30656 (PSB5_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Proteasome subunit beta type-5
EC=3.4.25.1

Alternative name(s):
Macropain subunit PRE2
Multicatalytic endopeptidase complex subunit PRE2
Proteasome component PRE2
Proteinase YSCE subunit PRE2

Gene names

Name:	PRE2
Synonyms:	DOA3, PRG1
Ordered Locus Names:	YPR103W
ORF Names:	P8283.10

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	287 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. This unit is responsible of the chymotrypsin-like activity of the proteasome and is one of the principal target of the proteasome inhibitor bortezomib. This subunit is necessary for chymotryptic activity and degradation of ubiquitinated proteins.
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-76 acts as nucleophile, and the N-terminal amino group acts as proton acceptor. Present with 8530 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the peptidase T1B family.
Sequence caution	The sequence CAA82203.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Cellular component	Cytoplasm Nucleus Proteasome
Molecular function	Hydrolase Protease Threonine protease
PTM	Phosphoprotein Zymogen
Technical term	3D-structure Complete proteome Direct protein sequencing 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 proteasome core complex assembly Inferred from mutant phenotype PubMed 8808631. Source: SGD
Cellular_component	endoplasmic reticulum membrane Inferred by curator Ref.9. Source: SGD nucleus Inferred by curator Ref.9. Source: SGD proteasome core complex, beta-subunit complex Inferred from direct assay Ref.9. Source: SGD proteasome storage granule Inferred by curator Ref.9. Source: SGD
Molecular_function	endopeptidase activity Inferred from mutant phenotype PubMed 8808631PubMed 9312134. Source: SGD threonine-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PRE1	P22141	3	EBI-14001,EBI-13988

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Propeptide

1 – 75

75

Removed in mature form

PRO_0000026611

Chain

76 – 287

212

Proteasome subunit beta type-5

PRO_0000026612

Sites

Active site

76

1

Nucleophile Ref.9

Binding site

124

1

Bortezomib; via amide nitrogen

Amino acid modifications

Modified residue

51

1

Phosphoserine Ref.8

Experimental info

Mutagenesis

126

1

D → N in DOA3-1; decrease in activity. Ref.3

Sequence conflict

282 – 287

6

FNNVIG → STTLLAK in AAA34906. Ref.1

Secondary structure

1

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287

Helix Strand Turn

Details...

Beta strand

78 – 83

6

Beta strand

86 – 91

6

Beta strand

95 – 97

3

Beta strand

100 – 104

5

Beta strand

109 – 113

5

Beta strand

116 – 119

4

Beta strand

121 – 123

3

Helix

124 – 145

22

Helix

151 – 164

14

Turn

165 – 167

3

Beta strand

172 – 180

9

Turn

181 – 183

3

Beta strand

184 – 191

8

Turn

192 – 194

3

Beta strand

196 – 198

3

Beta strand

200 – 205

6

Helix

208 – 218

11

Helix

225 – 242

18

Beta strand

243 – 246

4

Beta strand

248 – 256

9

Beta strand

259 – 267

9

Helix

268 – 279

12

Sequences

	Sequence		Length	Mass (Da)
	P30656 [UniParc]. Last modified February 1, 1995. Version 3. Checksum: D0EBAC611F7A4F37	FASTA	287	31,637
	10 20 30 40 50 60 MQAIADSFSV PNRLVKELQY DNEQNLESDF VTGASQFQRL APSLTVPPIA SPQQFLRAHT 70 80 90 100 110 120 DDSRNPDCKI KIAHGTTTLA FRFQGGIIVA VDSRATAGNW VASQTVKKVI EINPFLLGTM 130 140 150 160 170 180 AGGAADCQFW ETWLGSQCRL HELREKERIS VAAASKILSN LVYQYKGAGL SMGTMICGYT 190 200 210 220 230 240 RKEGPTIYYV DSDGTRLKGD IFCVGSGQTF AYGVLDSNYK WDLSVEDALY LGKRSILAAA 250 260 270 280 HRDAYSGGSV NLYHVTEDGW IYHGNHDVGE LFWKVKEEEG SFNNVIG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A homolog of the proteasome-related RING10 gene is essential for yeast cell growth." Friedman H., Goebel M., Snyder M. Gene 122:203-206(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"PRE2, highly homologous to the human major histocompatibility complex-linked RING10 gene, codes for a yeast proteasome subunit necessary for chrymotryptic activity and degradation of ubiquitinated proteins." Heinemeyer W., Gruhler A., Moehrle V., Mahe Y., Wolf D.H. J. Biol. Chem. 268:5115-5120(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 5288C.
[3]	"Biogenesis, structure and function of the yeast 20S proteasome." Chen P., Hochstrasser M. EMBO J. 14:2620-2630(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 76-90, MUTAGENESIS OF ASP-126.
[4]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI." Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M. , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J. Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[6]	"Suppression of yeast RNA polymerase III mutations by FHL1, a gene coding for a fork head protein involved in rRNA processing." Hermann-Ledenmat S., Werner M., Sentenac A., Thuriaux P. Mol. Cell. Biol. 14:2905-2913(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 176-287. Strain: ATCC 28383 / FL100 / VTT C-80102.
[7]	"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].
[8]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-51, MASS SPECTROMETRY.
[9]	"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 76-287 OF COMPLEX WITH THE 20S PROTEASOME, PROTEOLYTIC PROCESSING, ACTIVE SITE.
[10]	"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 76-287 OF COMPLEX WITH THE 20S PROTEASOME AND A 11S REGULATORY COMPLEX.
[11]	"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 76-287 OF COMPLEX WITH THE 20S PROTEASOME.
[12]	"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 76-287 OF COMPLEX WITH THE 20S PROTEASOME AND A TMC-95-BASED INHIBITOR.
[13]	"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 76-287 OF COMPLEX WITH THE 20S PROTEASOME AND SALINOSPORAMIDE.
[14]	"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 76-287 OF COMPLEX WITH THE 20S PROTEASOME AND BORTEZOMIB.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M96667 Genomic DNA. Translation: AAA34906.1.
X68662 Genomic DNA. Translation: CAA48628.1.
U32445 Genomic DNA. Translation: AAB68073.1.
Z28348 Genomic DNA. Translation: CAA82203.1. Different initiation.
BK006949 Genomic DNA. Translation: DAA11517.1.

PIR

A45411.

RefSeq

NP_015428.1. NM_001184200.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FNT	X-ray	3.20	L/Z	76-287	[»]
1G0U	X-ray	2.40	K/Y	76-287	[»]
1G65	X-ray	2.25	K/Y	76-287	[»]
1JD2	X-ray	3.00	K/R	76-287	[»]
1RYP	X-ray	1.90	L/Z	76-287	[»]
1VSY	X-ray	3.00	L/Z	76-287	[»]
1Z7Q	X-ray	3.22	L/Z	76-287	[»]
2F16	X-ray	2.80	K/Y	76-287	[»]
2FAK	X-ray	2.80	K/Y	76-287	[»]
2GPL	X-ray	2.81	K/Y	76-287	[»]
2ZCY	X-ray	2.90	K/Y	76-287	[»]
3BDM	X-ray	2.70	K/Y	76-287	[»]
3D29	X-ray	2.60	K/Y	76-287	[»]
3DY3	X-ray	2.81	K/Y	76-287	[»]
3DY4	X-ray	2.80	K/Y	76-287	[»]
3E47	X-ray	3.00	K/Y	76-287	[»]
3GPJ	X-ray	2.70	K/Y	76-287	[»]
3GPT	X-ray	2.41	K/Y	76-287	[»]
3GPW	X-ray	2.50	K/Y	76-287	[»]
3HYE	X-ray	2.50	K/Y	76-287	[»]
3L5Q	X-ray	3.00	2/P	76-287	[»]
3MG0	X-ray	2.68	K/Y	76-287	[»]
3MG4	X-ray	3.11	K/Y	76-287	[»]
3MG6	X-ray	2.60	K/Y	76-287	[»]
3MG7	X-ray	2.78	K/Y	76-287	[»]
3MG8	X-ray	2.59	K/Y	76-287	[»]
3NZJ	X-ray	2.40	K/Y	1-287	[»]
3NZW	X-ray	2.50	K/Y	1-287	[»]
3NZX	X-ray	2.70	K/Y	1-287	[»]
3OEU	X-ray	2.60	K/Y	76-287	[»]
3OEV	X-ray	2.85	K/Y	76-287	[»]
3OKJ	X-ray	2.70	K/Y	76-287	[»]
3SDI	X-ray	2.65	K/Y	76-287	[»]
3SDK	X-ray	2.70	K/Y	76-287	[»]
3SHJ	X-ray	2.80	K/Y	76-287	[»]
3TDD	X-ray	2.70	K/Y	76-287	[»]
3UN4	X-ray	3.40	K/Y	76-287	[»]
3UN8	X-ray	2.70	K/Y	76-287	[»]
4B4T	electron microscopy	7.40	5	1-287	[»]
4FZC	X-ray	2.80	K/Y	76-287	[»]
4FZG	X-ray	3.00	K/Y	76-287	[»]
4G4S	X-ray	2.49	L	76-287	[»]
4GK7	X-ray	2.80	K/Y	76-287	[»]
4INR	X-ray	2.70	K/Y	76-287	[»]
4INT	X-ray	2.90	K/Y	76-287	[»]
4INU	X-ray	3.10	K/Y	76-287	[»]

ProteinModelPortal

P30656.

SMR

P30656. Positions 49-287.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2806N.

IntAct

P30656. 20 interactions.

MINT

MINT-489734.

STRING

4932.YPR103W.

Protein family/group databases

MEROPS

T01.012.

Proteomic databases

PaxDb

P30656.

PeptideAtlas

P30656.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YPR103W; YPR103W; YPR103W.

GeneID

856218.

KEGG

sce:YPR103W.

Organism-specific databases

CYGD

YPR103w.

SGD

S000006307. PRE2.

Phylogenomic databases

eggNOG

COG0638.

GeneTree

ENSGT00510000046395.

HOGENOM

HOG000091082.

KO

K02737.

OMA

QTFAYGV.

OrthoDB

EOG47WRXH.

Gene expression databases

Genevestigator

P30656.

GermOnline

YPR103W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

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

Pfam

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

BindingDB

P30656.

ChEMBL

CHEMBL4659.

EvolutionaryTrace

P30656.

NextBio

981441.

Entry information

Entry name

PSB5_YEAST

Accession

Primary (citable) accession number: P30656
Secondary accession number(s): D6W4A1

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1993
Last sequence update:	February 1, 1995
Last modified:	May 1, 2013
This is version 138 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program