UniProt Accession

 RL401_YEAST; P0CH08; D6VVD9; P04838; P14796; P61864; Q6LA96 

Genbank Protein ID

 X05728; X05729; Z38059; BK006942 

Genbank Nucleotide ID

 CAA29195.1; CAA29196.1; CAA86130.1; DAA08405.1 

Protein Name

 Ubiquitin-60S ribosomal protein L40 

Protein Synonyms/Alias

 Ubiquitin; 60S ribosomal protein L40; CEP52 

Gene Name

 RPL40A 

Gene Synonyms/Alias

 UBI1; YIL148W 

Created Date

 July 27, 2013 

Organism

 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 

NCBI Taxa ID

 559292 

Lysine Modification

Position	Peptide	Type	References
6	**MQIFVKTLTGKTI	ubiquitination	[1]
11	FVKTLTGKTITLEVE	ubiquitination	[1, 2]
27	SDTIDNVKSKIQDKE	ubiquitination	[1, 2]
29	TIDNVKSKIQDKEGI	ubiquitination	[1, 2]
48	QRLIFAGKQLEDGRT	ubiquitination	[1, 2]
63	LSDYNIQKESTLHLV	ubiquitination	[1, 2]
83	GIIEPSLKALASKYN	ubiquitination	[3]
88	SLKALASKYNCDKSV	acetylation	[4]
88	SLKALASKYNCDKSV	ubiquitination	[2, 3]
93	ASKYNCDKSVCRKCY	ubiquitination	[2, 3]

Reference

 [1] A proteomics approach to understanding protein ubiquitination.
 Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP.
 Nat Biotechnol. 2003 Aug;21(8):921-6. [PMID: 12872131]
 [2] Sites of ubiquitin attachment in Saccharomyces cerevisiae.
 Starita LM, Lo RS, Eng JK, von Haller PD, Fields S.
 Proteomics. 2012 Jan;12(2):236-40. [PMID: 22106047]
 [3] Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
 Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.
 Nat Methods. 2013 Jul;10(7):676-82. [PMID: 23749301]
 [4] Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae.
 Henriksen P, Wagner SA, Weinert BT, Sharma S, Bacinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C.
 Mol Cell Proteomics. 2012 Nov;11(11):1510-22. [PMID: 22865919] 

Functional Description

 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). 

Sequence Annotation

 DOMAIN 1 76 Ubiquitin-like.
 MOD_RES 57 57 Phosphoserine.
 CROSSLNK 6 6 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 11 11 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 27 27 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 29 29 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 33 33 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 48 48 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 63 63 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 76 76 Glycyl lysine isopeptide (Gly-Lys)  

Keyword

 3D-structure; Complete proteome; Cytoplasm; DNA damage; DNA repair; Isopeptide bond; Nucleus; Phosphoprotein; Reference proteome; Ribonucleoprotein; Ribosomal protein; Ubl conjugation. 

Sequence Source

 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 

Protein Length

 128 AA 

Protein Sequence

Gene Ontology

 GO:0022625; C:cytosolic large ribosomal subunit; TAS:SGD.
 GO:0005634; C:nucleus; IDA:SGD.
 GO:0031386; F:protein tag; ISS:SGD.
 GO:0003735; F:structural constituent of ribosome; TAS:SGD.
 GO:0002181; P:cytoplasmic translation; TAS:SGD.
 GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
 GO:0016567; P:protein ubiquitination; IMP:SGD.
 GO:0042254; P:ribosome biogenesis; IDA:SGD. 

Interpro

 IPR001975; Ribosomal_L40e.
 IPR000626; Ubiquitin.
 IPR019954; Ubiquitin_CS.
 IPR019956; Ubiquitin_subgr.
 IPR019955; Ubiquitin_supergroup. 

Pfam

 PF01020; Ribosomal_L40e
 PF00240; ubiquitin 

SMART

 SM00213; UBQ 

PROSITE

 PS00299; UBIQUITIN_1
 PS50053; UBIQUITIN_2 

PRINTS

 PR00348; UBIQUITIN.