CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-002288
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Ubiquitin-40S ribosomal protein S31 
Protein Synonyms/Alias
 Ubiquitin; 40S ribosomal protein S31; CEP76; S37; YS24 
Gene Name
 RPS31 
Gene Synonyms/Alias
 RPS37; UBI3; YLR167W; L9470.14 
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**MQIFVKTLTGKTIubiquitination[1]
11FVKTLTGKTITLEVEubiquitination[1, 2, 3, 4, 5]
27SDTIDNVKSKIQDKEubiquitination[1, 4, 5]
33VKSKIQDKEGIPPDQubiquitination[1, 4]
48QRLIFAGKQLEDGRTacetylation[6]
48QRLIFAGKQLEDGRTubiquitination[1, 3, 4, 5]
63LSDYNIQKESTLHLVubiquitination[1, 3, 4, 5]
99KHKHKKVKLAVLSYYacetylation[6]
99KHKHKKVKLAVLSYYubiquitination[1, 7]
107LAVLSYYKVDAEGKVacetylation[6]
107LAVLSYYKVDAEGKVubiquitination[1]
113YKVDAEGKVTKLRREubiquitination[1]
136GVFLANHKDRLYCGKubiquitination[1]
143KDRLYCGKCHSVYKVubiquitination[1]
149GKCHSVYKVNA****ubiquitination[1, 7]
Reference
 [1] 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]
 [2] 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]
 [3] A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery.
 Hitchcock AL, Auld K, Gygi SP, Silver PA.
 Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12735-40. [PMID: 14557538]
 [4] Systematic approach for validating the ubiquitinated proteome.
 Seyfried NT, Xu P, Duong DM, Cheng D, Hanfelt J, Peng J.
 Anal Chem. 2008 Jun 1;80(11):4161-9. [PMID: 18433149]
 [5] A perturbed ubiquitin landscape distinguishes between ubiquitin in trafficking and in proteolysis.
 Ziv I, Matiuhin Y, Kirkpatrick DS, Erpapazoglou Z, Leon S, Pantazopoulou M, Kim W, Gygi SP, Haguenauer-Tsapis R, Reis N, Glickman MH, Kleifeld O.
 Mol Cell Proteomics. 2011 May;10(5):M111.009753. [PMID: 21427232]
 [6] 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]
 [7] 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] 
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.
 ZN_FING 121 144 C4-type.
 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; Direct protein sequencing; DNA damage; DNA repair; Isopeptide bond; Metal-binding; Nucleus; Phosphoprotein; Reference proteome; Ribonucleoprotein; Ribosomal protein; Ubl conjugation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 152 AA 
Protein Sequence
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN 60
IQKESTLHLV LRLRGGGKKR KKKVYTTPKK IKHKHKKVKL AVLSYYKVDA EGKVTKLRRE 120
CSNPTCGAGV FLANHKDRLY CGKCHSVYKV NA 152 
Gene Ontology
 GO:0022627; C:cytosolic small ribosomal subunit; IDA:SGD.
 GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0031386; F:protein tag; IMP:SGD.
 GO:0003735; F:structural constituent of ribosome; IC:SGD.
 GO:0002181; P:cytoplasmic translation; IC:SGD.
 GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
 GO:0002109; P:maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S); IMP:SGD.
 GO:0000028; P:ribosomal small subunit assembly; IMP:SGD. 
Interpro
 IPR002906; Ribosomal_S27a.
 IPR000626; Ubiquitin.
 IPR019954; Ubiquitin_CS.
 IPR019956; Ubiquitin_subgr.
 IPR019955; Ubiquitin_supergroup. 
Pfam
 PF01599; Ribosomal_S27
 PF00240; ubiquitin 
SMART
 SM00213; UBQ 
PROSITE
 PS00299; UBIQUITIN_1
 PS50053; UBIQUITIN_2 
PRINTS
 PR00348; UBIQUITIN.