P40303 (PSA4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Proteasome subunit alpha type-4
EC=3.4.25.1

Alternative name(s):
Macropain subunit PRE6
Multicatalytic endopeptidase complex subunit PRE6
Proteasome component PRE6
Proteinase YSCE subunit PRE6

Gene names

Name:	PRE6
Ordered Locus Names:	YOL038W

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	254 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. Interacts with CIC1. Ref.5
Subcellular location	Cytoplasm. Nucleus Ref.6.
Miscellaneous	Present with 16800 molecules/cell in log phase SD medium.
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 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
Cellular_component	mitochondrion Inferred from direct assay PubMed 16806052. Source: SGD nuclear outer membrane-endoplasmic reticulum membrane network Inferred from direct assay PubMed 9799224. Source: SGD nucleus Inferred from direct assay PubMed 18504300. Source: SGD proteasome core complex, alpha-subunit complex Inferred from direct assay Ref.10. Source: SGD proteasome storage granule Inferred from direct assay PubMed 18504300. Source: SGD
Molecular_function	threonine-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CIC1	P38779	5	EBI-13980,EBI-24538
cut8	P38937	2	EBI-13980,EBI-1152591	From a different organism.
PRE1	P22141	3	EBI-13980,EBI-13988

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 254

254

Proteasome subunit alpha type-4

PRO_0000124165

Amino acid modifications

Modified residue

60

1

Phosphothreonine Ref.8

Modified residue

69

1

Phosphoserine Ref.9

Secondary structure

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254

Helix Strand Turn

Details...

Beta strand

7 – 10

4

Turn

13 – 15

3

Helix

18 – 27

10

Beta strand

33 – 37

5

Beta strand

42 – 47

6

Beta strand

53 – 55

3

Turn

57 – 59

3

Beta strand

63 – 68

6

Beta strand

71 – 77

7

Helix

79 – 100

22

Helix

106 – 119

14

Turn

120 – 122

3

Beta strand

123 – 126

4

Beta strand

130 – 137

8

Beta strand

146 – 150

5

Turn

152 – 154

3

Beta strand

156 – 165

10

Helix

168 – 176

9

Beta strand

181 – 183

3

Helix

188 – 203

16

Beta strand

204 – 206

3

Helix

207 – 209

3

Beta strand

210 – 216

7

Turn

217 – 219

3

Beta strand

220 – 223

4

Helix

226 – 236

11

Helix

238 – 241

4

Sequences

	Sequence		Length	Mass (Da)
	P40303 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: 73AEE63B836E618A	FASTA	254	28,439
	10 20 30 40 50 60 MSGYDRALSI FSPDGHIFQV EYALEAVKRG TCAVGVKGKN CVVLGCERRS TLKLQDTRIT 70 80 90 100 110 120 PSKVSKIDSH VVLSFSGLNA DSRILIEKAR VEAQSHRLTL EDPVTVEYLT RYVAGVQQRY 130 140 150 160 170 180 TQSGGVRPFG VSTLIAGFDP RDDEPKLYQT EPSGIYSSWS AQTIGRNSKT VREFLEKNYD 190 200 210 220 230 240 RKEPPATVEE CVKLTVRSLL EVVQTGAKNI EITVVKPDSD IVALSSEEIN QYVTQIEQEK 250 QEQQEQDKKK KSNH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"PRE5 and PRE6, the last missing genes encoding 20S proteasome subunits from yeast? Indication for a set of 14 different subunits in the eukaryotic proteasome core." Heinemeyer W., Troendle N., Albrecht G., Wolf D.H. Biochemistry 33:12229-12237(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	"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: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	Troendle N. Thesis (1991), University of Stuttgart, Germany Cited for: PROTEIN SEQUENCE OF 112-133.
[5]	"Cic1, an adaptor protein specifically linking the 26S proteasome to its substrate, the SCF component Cdc4." Jaeger S., Strayle J., Heinemeyer W., Wolf D.H. EMBO J. 20:4423-4431(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH CIC1.
[6]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[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]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-60, MASS SPECTROMETRY.
[9]	"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-69, MASS SPECTROMETRY.
[10]	"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 3-343 OF COMPLEX WITH THE 20S PROTEASOME.
[11]	"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 COMPLEX WITH THE 20S PROTEASOME.
[12]	"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 1-243 OF COMPLEX WITH THE 20S PROTEASOME.
[13]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 3-243 OF COMPLEX WITH THE 20S PROTEASOME.
[14]	"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 3-243 OF COMPLEX WITH THE 20S PROTEASOME.
[15]	"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 3-243 OF COMPLEX WITH THE 20S PROTEASOME.
[16]	"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 3-243 OF COMPLEX WITH THE 20S PROTEASOME.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L34348 Genomic DNA. Translation: AAA34903.1.
Z74780 Genomic DNA. Translation: CAA99040.1.
BK006948 Genomic DNA. Translation: DAA10745.1.

PIR

B55904.

RefSeq

NP_014604.1. NM_001183292.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FNT	X-ray	3.20	D/R	1-254	[»]
1G0U	X-ray	2.40	C/Q	1-243	[»]
1G65	X-ray	2.25	C/Q	3-243	[»]
1JD2	X-ray	3.00	C/X	3-243	[»]
1RYP	X-ray	1.90	D/R	3-243	[»]
1VSY	X-ray	3.00	D/R	17-243	[»]
1Z7Q	X-ray	3.22	D/R	1-254	[»]
2F16	X-ray	2.80	C/Q	3-243	[»]
2FAK	X-ray	2.80	C/Q	3-243	[»]
2GPL	X-ray	2.81	C/Q	3-243	[»]
2ZCY	X-ray	2.90	C/Q	1-254	[»]
3BDM	X-ray	2.70	C/Q	1-254	[»]
3D29	X-ray	2.60	C/Q	3-236	[»]
3DY3	X-ray	2.81	C/Q	3-243	[»]
3DY4	X-ray	2.80	C/Q	3-243	[»]
3E47	X-ray	3.00	C/Q	3-243	[»]
3GPJ	X-ray	2.70	C/Q	3-243	[»]
3GPT	X-ray	2.41	C/Q	3-243	[»]
3GPW	X-ray	2.50	C/Q	3-243	[»]
3HYE	X-ray	2.50	C/Q	3-243	[»]
3L5Q	X-ray	3.00	I/U	17-243	[»]
3MG0	X-ray	2.68	C/Q	3-243	[»]
3MG4	X-ray	3.11	C/Q	3-243	[»]
3MG6	X-ray	2.60	C/Q	1-243	[»]
3MG7	X-ray	2.78	C/Q	1-243	[»]
3MG8	X-ray	2.59	C/Q	1-243	[»]
3NZJ	X-ray	2.40	C/Q	1-254	[»]
3NZW	X-ray	2.50	C/Q	1-254	[»]
3NZX	X-ray	2.70	C/Q	1-254	[»]
3OEU	X-ray	2.60	C/Q	3-243	[»]
3OEV	X-ray	2.85	C/Q	3-243	[»]
3OKJ	X-ray	2.70	C/Q	3-243	[»]
3SDI	X-ray	2.65	C/Q	3-243	[»]
3SDK	X-ray	2.70	C/Q	3-243	[»]
3SHJ	X-ray	2.80	C/Q	3-243	[»]
3TDD	X-ray	2.70	C/Q	3-243	[»]
3UN4	X-ray	3.40	C/Q	1-254	[»]
3UN8	X-ray	2.70	C/Q	1-254	[»]
4B4T	electron microscopy	7.40	D	1-254	[»]
4FZC	X-ray	2.80	C/Q	3-243	[»]
4FZG	X-ray	3.00	C/Q	3-243	[»]
4G4S	X-ray	2.49	D	1-254	[»]
4GK7	X-ray	2.80	C/Q	3-243	[»]
4INR	X-ray	2.70	C/Q	1-254	[»]
4INT	X-ray	2.90	C/Q	1-254	[»]
4INU	X-ray	3.10	C/Q	1-254	[»]

ProteinModelPortal

P40303.

SMR

P40303. Positions 3-243.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-4844N.

IntAct

P40303. 39 interactions.

MINT

MINT-478854.

STRING

4932.YOL038W.

Protein family/group databases

MEROPS

T01.974.

Proteomic databases

PaxDb

P40303.

PeptideAtlas

P40303.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOL038W; YOL038W; YOL038W.

GeneID

854119.

KEGG

sce:YOL038W.

Organism-specific databases

CYGD

YOL038w.

SGD

S000005398. PRE6.

Phylogenomic databases

eggNOG

COG0638.

GeneTree

ENSGT00550000074753.

HOGENOM

HOG000091085.

KO

K02731.

OMA

NRAQVEC.

OrthoDB

EOG45B4QP.

Enzyme and pathway databases

BioCyc

YEAST:G3O-33452-MONOMER.

Gene expression databases

Genevestigator

P40303.

GermOnline

YOL038W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR000426. Proteasome_asu_N.
IPR016050. Proteasome_bsu_CS.
IPR023332. Proteasome_suA-type.
IPR001353. Proteasome_sua/b.
[Graphical view]

Pfam

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

SMART

SM00948. 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

EvolutionaryTrace

P40303.

NextBio

975822.

Entry information

Entry name

PSA4_YEAST

Accession

Primary (citable) accession number: P40303
Secondary accession number(s): D6W229

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	May 29, 2013
This is version 140 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program