CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-007834
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 40S ribosomal protein S9 
Protein Synonyms/Alias
  
Gene Name
 RPS9 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
11ARSWVCRKTYVTPRRubiquitination[1]
22TPRRPFEKSRLDQELubiquitination[2, 3]
30SRLDQELKLIGEYGLubiquitination[1, 2, 3, 4, 5]
47KREVWRVKFTLAKIRubiquitination[1]
52RVKFTLAKIRKAAREubiquitination[4]
66ELLTLDEKDPRRLFEubiquitination[1, 2, 3, 5]
91IGVLDEGKMKLDYILubiquitination[1, 2, 5]
93VLDEGKMKLDYILGLubiquitination[1, 2, 4, 5, 6]
101LDYILGLKIEDFLERubiquitination[2]
116RLQTQVFKLGLAKSIubiquitination[1, 4]
121VFKLGLAKSIHHARVubiquitination[1, 2, 5, 6, 7]
139QRHIRVRKQVVNIPSubiquitination[1, 2, 4, 8]
155IVRLDSQKHIDFSLRacetylation[8, 9, 10]
155IVRLDSQKHIDFSLRubiquitination[1, 2, 3, 4, 5, 6, 8, 11]
180VKRKNAKKGQGGAGAubiquitination[2]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [3] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [4] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [5] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [6] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
 Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048]
 [7] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [8] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [9] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
 [10] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [11] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094] 
Functional Description
  
Sequence Annotation
 DOMAIN 108 182 S4 RNA-binding.
 MOD_RES 155 155 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Complete proteome; Cytoplasm; Direct protein sequencing; Polymorphism; Reference proteome; Ribonucleoprotein; Ribosomal protein; RNA-binding; rRNA-binding. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 194 AA 
Protein Sequence
MPVARSWVCR KTYVTPRRPF EKSRLDQELK LIGEYGLRNK REVWRVKFTL AKIRKAAREL 60
LTLDEKDPRR LFEGNALLRR LVRIGVLDEG KMKLDYILGL KIEDFLERRL QTQVFKLGLA 120
KSIHHARVLI RQRHIRVRKQ VVNIPSFIVR LDSQKHIDFS LRSPYGGGRP GRVKRKNAKK 180
GQGGAGAGDD EEED 194 
Gene Ontology
 GO:0022627; C:cytosolic small ribosomal subunit; IDA:UniProtKB.
 GO:0005730; C:nucleolus; IDA:UniProtKB.
 GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
 GO:0003735; F:structural constituent of ribosome; IEA:InterPro.
 GO:0045182; F:translation regulator activity; IMP:UniProtKB.
 GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; TAS:Reactome.
 GO:0008284; P:positive regulation of cell proliferation; IMP:UniProtKB.
 GO:0006614; P:SRP-dependent cotranslational protein targeting to membrane; TAS:Reactome.
 GO:0006414; P:translational elongation; TAS:Reactome.
 GO:0006413; P:translational initiation; TAS:Reactome.
 GO:0006415; P:translational termination; TAS:Reactome.
 GO:0019083; P:viral transcription; TAS:Reactome. 
Interpro
 IPR022801; Ribosomal_S4/S9.
 IPR005710; Ribosomal_S4/S9_euk/arc.
 IPR001912; Ribosomal_S4/S9_N.
 IPR018079; Ribosomal_S4_CS.
 IPR002942; S4_RNA-bd. 
Pfam
 PF00163; Ribosomal_S4
 PF01479; S4 
SMART
 SM00363; S4 
PROSITE
 PS00632; RIBOSOMAL_S4
 PS50889; S4 
PRINTS