Ubiquitin-60S ribosomal protein L40 precursor - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P0CH08 (RL401_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 24. History...

Clusters with 100%, 90%, 50% identity |

Documents (5) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Ubiquitin-60S ribosomal protein L40

Cleaved into the following 2 chains:

Ubiquitin
60S ribosomal protein L40
Alternative name(s):
CEP52

Gene names

Name:	RPL40A
Synonyms:	UBI1
Ordered Locus Names:	YIL148W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	128 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	Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling By similarity. Ribosomal protein L40 is a component of the 60S subunit of the ribosome.
Subunit structure	Ribosomal protein L40 is part of the 60S ribosomal subunit. Mature ribosomes consist of a small (40S) and a large (60S) subunit. The 40S subunit contains 32 different proteins (encoded by 56 genes) and 1 molecule of RNA (18S). The 60S subunit contains 46 different proteins (encoded by 81 genes) and 3 molecules of RNA (25S, 5.8S and 5S). Ref.7
Subcellular location	Ubiquitin: Cytoplasm By similarity. Nucleus By similarity Ref.8. 60S ribosomal protein L40: Cytoplasm Ref.8.
Miscellaneous	Ubiquitin is encoded by 4 different genes. UBI1 and UBI2 genes code for a single copy of ubiquitin fused to the ribosomal proteins 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. The 60S ribosomal protein L40 is present with 40000 molecules/cell in log phase SD medium.
Sequence similarities	In the N-terminal section; belongs to the ubiquitin family. In the C-terminal section; belongs to the ribosomal protein L40e family. Contains 1 ubiquitin-like domain.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Cytoplasm Nucleus
Molecular function	Ribonucleoprotein Ribosomal protein
PTM	Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW cytoplasmic translation Traceable author statement Ref.7. Source: SGD protein ubiquitination Inferred from mutant phenotype PubMed 8035826. Source: SGD ribosome biogenesis Inferred from direct assay PubMed 2538753. Source: SGD
Cellular_component	cytosolic large ribosomal subunit Traceable author statement Ref.7. Source: SGD nucleus Inferred from direct assay PubMed 22842922. Source: SGD
Molecular_function	protein tag Inferred from sequence or structural similarity Ref.1. Source: SGD structural constituent of ribosome Traceable author statement Ref.7. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 76

Ubiquitin

PRO_0000396454

Chain

77 – 128

60S ribosomal protein L40

PRO_0000138775

Regions

Domain

1 – 76

Ubiquitin-like

Amino acid modifications

Modified residue

Phosphoserine Ref.4 Ref.11

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4 Ref.10

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4 Ref.10

Cross-link

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.4 Ref.10

Cross-link

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

Experimental info

Mutagenesis

K → R: Deficiency in ubiquitin-protein conjugate formation. Ref.5 Ref.6

Mutagenesis

K → R: Deficiency in ubiquitin-protein conjugate formation. Ref.5 Ref.6

Mutagenesis

K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. Ref.5 Ref.6

Sequences

Sequence

Length

Mass (Da)

Tools

P0CH08 [UniParc].

Last modified August 10, 2010. Version 1.
Checksum: 84BD137A4B1F7797
Show »

FASTA

128

14,554

        10         20         30         40         50         60 
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN 

        70         80         90        100        110        120 
IQKESTLHLV LRLRGGIIEP SLKALASKYN CDKSVCRKCY ARLPPRATNC RKRKCGHTNQ 


LRPKKKLK

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"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. Barrell B.G. Nature 387:84-87(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"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] [Europe PMC] [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 (UBIQUITIN). Strain: SUB592.
[5]	"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] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF LYS-29; LYS-48 AND LYS-63.
[6]	"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] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF LYSINE RESIDUES IN UBIQUITIN.
[7]	"The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae." Planta R.J., Mager W.H. Yeast 14:471-477(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NOMENCLATURE, SUBUNIT (L40).
[8]	"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] (L40).
[9]	"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] (L40).
[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] [Europe PMC] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-11; LYS-48 AND LYS-63, MASS SPECTROMETRY (UBIQUITIN).
[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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-57, MASS SPECTROMETRY (UBIQUITIN).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X05728 Genomic DNA. Translation: CAA29195.1.
X05729 Genomic DNA. Translation: CAA29196.1.
Z38059 Genomic DNA. Translation: CAA86130.1.
BK006942 Genomic DNA. Translation: DAA08405.1.

PIR

A29456.

RefSeq

NP_012118.1. NM_001179496.1.
NP_013020.3. NM_001179884.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3IZS	electron microscopy	-	p	77-128	[»]
3U5E	X-ray	3.00	m	1-128	[»]
3U5I	X-ray	3.00	m	1-128	[»]
4B6A	electron microscopy	8.10	m	1-128	[»]

ProteinModelPortal

P0CH08.

SMR

P0CH08. Positions 1-74, 77-128.

ModBase

Search...

2D gel databases

SWISS-2DPAGE

P61864.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YIL148W; YIL148W; YIL148W.
YKR094C; YKR094C; YKR094C.

GeneID

853969.
854658.

KEGG

sce:YIL148W.
sce:YKR094C.
sce:YKR095W-A.

Organism-specific databases

SGD

S000001410. RPL40A.

Phylogenomic databases

K02927.
K15902.

OrthoDB

EOG48WGBH.

Gene expression databases

ArrayExpress

P0CH08.

Genevestigator

P61864.

GermOnline

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

Family and domain databases

InterPro

IPR001975. Ribosomal_L40e.
IPR000626. Ubiquitin.
IPR019954. Ubiquitin_CS.
IPR019956. Ubiquitin_subgr.
IPR019955. Ubiquitin_supergroup.
[Graphical view]

Pfam

PF01020. Ribosomal_L40e. 1 hit.
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...

Other

NextBio

975410.

Entry information

Entry name

RL401_YEAST

Accession

Primary (citable) accession number: P0CH08
Secondary accession number(s): D6VVD9

Q6LA96

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 10, 2010
Last sequence update:	August 10, 2010
Last modified:	April 3, 2013
This is version 24 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome IX

Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

Ribosomal proteins

Ribosomal proteins families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Cleaved into the following 2 chains:

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

2D gel databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents