Reviewed, UniProtKB/Swiss-Prot P61864 (UBIQ_YEAST)

Names and origin

Protein names

Recommended name:
    Ubiquitin

Gene names

Name:	UBI1
Synonyms:	RPL40A
Ordered Locus Names:	YIL148W
AND
Name:	UBI2
Synonyms:	RPL40B
Ordered Locus Names:	YKR094C
AND
Name:	UBI3
Synonyms:	RPS31
Ordered Locus Names:	YLR167W
ORF Names:	L9470.14
AND
Name:	UBI4
Synonyms:	SCD2
Ordered Locus Names:	YLL039C

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

General annotation (Comments)

Function	Protein modifier which can be covalently attached to target lysines either as a monomer or as a lysine-linked polymer. Attachment to proteins as a Lys-48-linked polymer usually leads to their degradation by proteasome. Attachment to proteins as a monomer or as an alternatively linked polymer does not lead to proteasomal degradation and may be required for numerous functions, including maintenance of chromatin structure, regulation of gene expression, stress response, ribosome biogenesis and DNA repair.
Subcellular location	Cytoplasm. Nucleus.
Post-translational modification	Several types of polymeric chains can be formed, depending on the lysine used for the assembly.
Miscellaneous	UBI1 and UBI2 are synthesized as a polyprotein with one copy of ubiquitin fused to ribosomal protein L40. UBI3 is a polyprotein with one copy of ubiquitin fused to ribosomal protein S37. UBI4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin, there is a final amino-acid (Asn) after the last repeat.
Sequence similarities	Belongs to the ubiquitin family.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Cytoplasm Nucleus
PTM	Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW protein ubiquitination Inferred from mutant phenotype. Source: SGD ribosome biogenesis Inferred from direct assay. Source: SGD translation Traceable author statement. Source: SGD
Cellular component	cytosolic large ribosomal subunit Traceable author statement. Source: SGD mitochondrion Inferred from direct assay. Source: SGD nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	protein binding Inferred from physical interaction. Source: IntAct structural constituent of ribosome Traceable author statement. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
	P43582	1	EBI-19797,EBI-22766
LSB5	P25369	1	EBI-19797,EBI-10218
PIB1	Q06651	1	EBI-19797,EBI-35947
Prkcb	P68403-2	1	EBI-19797,EBI-397092	From a different organism.
RAD17	P48581	1	EBI-19797,EBI-14652
STE6	P12866	1	EBI-19797,EBI-18383
UBA1	P22515	1	EBI-19797,EBI-19703
URN1	Q06525	1	EBI-19797,EBI-35138

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 76

76

Ubiquitin

PRO_0000114861

Amino acid modifications

Modified residue

57

1

Phosphoserine Ref.7 Ref.11

Cross-link

6

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7

Cross-link

11

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7 Ref.10

Cross-link

27

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7

Cross-link

29

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7

Cross-link

33

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7

Cross-link

48

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7 Ref.10

Cross-link

63

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7 Ref.10

Cross-link

76

Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Experimental info

Mutagenesis

29

1

K → R: Deficiency in ubiquitin-protein conjugate formation. Ref.8 Ref.9

Mutagenesis

48

1

K → R: Deficiency in ubiquitin-protein conjugate formation. Ref.8 Ref.9

Mutagenesis

63

1

K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. Ref.8 Ref.9

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

76

Helix Strand Turn

Details...

Beta strand

2 – 10

9

Beta strand

12 – 16

5

Helix

23 – 34

12

Turn

38 – 40

3

Beta strand

41 – 45

5

Helix

56 – 59

4

Beta strand

66 – 71

6

Sequences

	Sequence		Length	Mass (Da)
	P61864-1 [UniParc]. Last modified August 13, 1987. Version 1. Checksum: 9AC936269D38403E	FASTA	76	8,557
	10 20 30 40 50 60 MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN 70 IQKESTLHLV LRLRGG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The yeast ubiquitin gene: head-to-tail repeats encoding a polyubiquitin precursor protein." Oezkaynak E., Finley D., Varshavsky A. Nature 312:663-666(1984) [PubMed: 6095120] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The yeast ubiquitin genes: a family of natural gene fusions." Oezkaynak E., Finley D., Solomon M.J., Varshavsky A. EMBO J. 6:1429-1439(1987) [PubMed: 3038523] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (UBI1; UBI2; UBI3 AND UBI4).
[3]	"The complete sequence of a 15,820 bp segment of Saccharomyces cerevisiae chromosome XI contains the UBI2 and MPL1 genes and three new open reading frames." Bou G., Esteban P.F., Baladron V., Gonzalez G.A., Cantalejo J.G., Remacha M.A., Jimenez A., del Rey F., Ballesta J.P.G., Revuelta J.L. Yeast 9:1349-1354(1993) [PubMed: 8154186] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (UBI2).
[4]	"Complete DNA sequence of yeast chromosome XI." Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W. Nature 369:371-378(1994) [PubMed: 8196765] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (UBI2). Strain: ATCC 96604 / S288c / FY1679.
[5]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX." Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D., Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E., Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C. , Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V., Walsh S.V., Whitehead S., Barrell B.G. Nature 387:84-87(1997) [PubMed: 9169870] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (UBI1). Strain: ATCC 204511 / S288c / AB972.
[6]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII." Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D. Nature 387:87-90(1997) [PubMed: 9169871] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (UBI3 AND UBI4). Strain: ATCC 204511 / S288c / AB972.
[7]	"A proteomics approach to understanding protein ubiquitination." Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P. Nat. Biotechnol. 21:921-926(2003) [PubMed: 12872131] [Abstract] Cited for: PROTEIN SEQUENCE OF 43-53, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-57, UBIQUITINATION AT LYS-6; LYS-11; LYS-27; LYS-29; LYS-33; LYS-48 AND LYS-63, MASS SPECTROMETRY.
[8]	"A proteolytic pathway that recognizes ubiquitin as a degradation signal." Johnson E.S., Ma P.C.M., Ota I.M., Varshavsky A. J. Biol. Chem. 270:17442-17456(1995) [PubMed: 7615550] [Abstract] Cited for: MUTAGENESIS OF LYS-29; LYS-48 AND LYS-63.
[9]	"A ubiquitin mutant with specific defects in DNA repair and multiubiquitination." Spence J., Sadis S., Haas A.L., Finley D. Mol. Cell. Biol. 15:1265-1273(1995) [PubMed: 7862120] [Abstract] Cited for: MUTAGENESIS OF LYSINE RESIDUES.
[10]	"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-11; LYS-48 AND LYS-63, MASS SPECTROMETRY.
[11]	"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-57, MASS SPECTROMETRY.
[12]	"Structural basis for the specificity of ubiquitin C-terminal hydrolases." Johnston S.C., Riddle S.M., Cohen R.E., Hill C.P. EMBO J. 18:3877-3887(1999) [PubMed: 10406793] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH YUH1.
[13]	"A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain." Shih S.C., Prag G., Francis S.A., Sutanto M.A., Hurley J.H., Hicke L. EMBO J. 22:1273-1281(2003) [PubMed: 12628920] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH VPS9.
[14]	"Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail." Hamilton K.S., Ellison M.J., Barber K.R., Williams R.S., Huzil J.T., McKenna S., Ptak C., Glover M., Shaw G.S. Structure 9:897-904(2001) [PubMed: 11591345] [Abstract] Cited for: STRUCTURE BY NMR IN COMPLEX WITH UBC1.
[15]	"Solution structure of a CUE-ubiquitin complex reveals a conserved mode of ubiquitin binding." Kang R.S., Daniels C.M., Francis S.A., Shih S.C., Salerno W.J., Hicke L., Radhakrishnan I. Cell 113:621-630(2003) [PubMed: 12787503] [Abstract] Cited for: STRUCTURE BY NMR OF COMPLEX WITH CUE2 N-TERMINAL DOMAIN.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X01473 Genomic DNA. Translation: CAA25704.1. Different termination.
X01474 Genomic DNA. Translation: CAA25706.1. Sequence problems.
X05728 Genomic DNA. Translation: CAA29195.1. Different termination.
X05729 Genomic DNA. Translation: CAA29196.1. Different termination.
X05730 Genomic DNA. Translation: CAA29197.1. Different termination.
X05731 Genomic DNA. Translation: CAA29198.1. Different termination.
X73541 Genomic DNA. Translation: CAA51949.1. Different termination.
Z28319 Genomic DNA. Translation: CAA82173.1. Different termination.
Z38059 Genomic DNA. Translation: CAA86130.1. Different termination.
U17246 Genomic DNA. Translation: AAB67466.1. Different termination.
Z73144 Genomic DNA. Translation: CAA97489.1. Different termination.

PIR

A29456.
UQBYR7. C29456.
UQBY. D29456.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1OTR	NMR	-	B	1-76	[»]
1Q0W	NMR	-	B	1-76	[»]
1WR1	NMR	-	A	1-76	[»]
1ZW7	NMR	-	A	1-76	[»]
2G3Q	NMR	-	B	1-76	[»]
2JT4	NMR	-	B	1-76	[»]
2JWZ	NMR	-	A	1-76	[»]
3CMM	X-ray	2.70	B/D	1-76	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P61864. 35 interactions.

2-D gel databases

SWISS-2DPAGE

P61864.

Proteomic databases

PeptideAtlas

P61864.

PRIDE

P61864.

Genome annotation databases

Ensembl

YIL148W. Saccharomyces cerevisiae. [Contig view]
YKR094C. Saccharomyces cerevisiae. [Contig view]
YLL039C. Saccharomyces cerevisiae. [Contig view]
YLR167W. Saccharomyces cerevisiae. [Contig view]

KEGG

sce:YIL148W.
sce:YKR094C.

Organism-specific databases

CYGD

YIL148w.
YKR094c.
YLL039c.
YLR167w.

SGD

S000001410. RPL40A.
S000001802. RPL40B.
S000004157. RPS31.
S000003962. UBI4.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P61864.

Gene expression databases

ArrayExpress

P61864.

GermOnline

YIL148W. Saccharomyces cerevisiae.
YKR094C. Saccharomyces cerevisiae.
YLL039C. Saccharomyces cerevisiae.
YLR167W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR000626. Ubiquitin.
IPR019954. Ubiquitin_CS.
IPR019956. Ubiquitin_subgroup.
IPR019955. Ubiquitin_supergroup.
[Graphical view]

Pfam

PF00240. ubiquitin. 1 hit.
[Graphical view]

PRINTS

PR00348. UBIQUITIN.

SMART

SM00213. UBQ. 1 hit.
[Graphical view]

PROSITE

PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

UBIQ_YEAST

Accession

Primary (citable) accession number: P61864
Secondary accession number(s): P04838, Q6LA96

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	August 13, 1987
Last modified:	June 16, 2009
This is version 70 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)