CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-005605
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Replication protein A 70 kDa DNA-binding subunit 
Protein Synonyms/Alias
 RP-A p70; Replication factor A protein 1; RF-A protein 1; Single-stranded DNA-binding protein; Replication protein A 70 kDa DNA-binding subunit, N-terminally processed 
Gene Name
 RPA1 
Gene Synonyms/Alias
 REPA1; RPA70 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
22QKGDTNIKPILQVINubiquitination[1, 2, 3, 4, 5, 6]
88RFIVNTLKDGRRVVIubiquitination[1, 2, 4, 6, 7]
157GMGSTVSKAYGASKTubiquitination[1, 6]
163SKAYGASKTFGKAAGacetylation[8, 9]
163SKAYGASKTFGKAAGubiquitination[1, 4, 5, 6, 9, 10]
167GASKTFGKAAGPSLSacetylation[8]
167GASKTFGKAAGPSLSubiquitination[1, 2, 3, 4, 5, 6, 7, 9, 10, 11]
183TSGGTQSKVVPIASLubiquitination[1, 3, 4, 6, 9, 11]
196SLTPYQSKWTICARVubiquitination[1, 3, 4, 6, 9]
244AFNEQVDKFFPLIEVubiquitination[1, 2, 4, 6, 7, 9, 11]
259NKVYYFSKGTLKIANacetylation[8]
267GTLKIANKQFTAVKNubiquitination[3, 4]
313DDLENKSKDSLVDIIubiquitination[4]
324VDIIGICKSYEDATKubiquitination[4]
331KSYEDATKITVRSNNubiquitination[4, 10]
367LWGEDADKFDGSRQPubiquitination[1, 4, 6]
379RQPVLAIKGARVSDFubiquitination[4]
410PDIPEAYKLRGWFDAubiquitination[1, 2, 3, 4, 5, 6, 7, 10, 12, 13, 14]
431GVSISDLKSGGVGGSubiquitination[2, 4, 5, 7, 10]
443GGSNTNWKTLYEVKSubiquitination[1, 4, 5, 6, 7]
449WKTLYEVKSENLGQGsumoylation[15]
449WKTLYEVKSENLGQGubiquitination[11]
458ENLGQGDKPDYFSSVubiquitination[2, 7]
473ATVVYLRKENCMYQAubiquitination[4]
488CPTQDCNKKVIDQQNubiquitination[4, 9, 10, 11]
489PTQDCNKKVIDQQNGacetylation[9]
489PTQDCNKKVIDQQNGubiquitination[1, 4, 6, 7, 9]
502NGLYRCEKCDTEFPNubiquitination[3, 4, 9, 10, 11, 14]
511DTEFPNFKYRMILSVubiquitination[4, 9, 11]
553YLGELKDKNEQAFEEubiquitination[2, 4, 5, 7]
577FIFRVRVKVETYNDEsumoylation[15]
577FIFRVRVKVETYNDEubiquitination[4, 5, 7]
588YNDESRIKATVMDVKubiquitination[1, 4, 5, 6, 7]
595KATVMDVKPVDYREYubiquitination[1, 4, 5, 6, 7, 14]
Reference
 [1] 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]
 [2] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
 Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
 J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931]
 [3] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [4] 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]
 [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] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [7] 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]
 [8] 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]
 [9] 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]
 [10] 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]
 [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]
 [12] Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling.
 Xu G, Paige JS, Jaffrey SR.
 Nat Biotechnol. 2010 Aug;28(8):868-73. [PMID: 20639865]
 [13] 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]
 [14] 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]
 [15] Regulation of DNA repair through deSUMOylation and SUMOylation of replication protein A complex.
 Dou H, Huang C, Singh M, Carpenter PB, Yeh ET.
 Mol Cell. 2010 Aug 13;39(3):333-45. [PMID: 20705237] 
Functional Description
 Plays an essential role in several cellular processes in DNA metabolism including replication, recombination and DNA repair. Binds and subsequently stabilizes single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. 
Sequence Annotation
 ZN_FING 481 503 C4-type (Potential).
 MOD_RES 1 1 N-acetylmethionine.
 MOD_RES 163 163 N6-acetyllysine.
 MOD_RES 167 167 N6-acetyllysine.
 MOD_RES 180 180 Phosphothreonine.
 MOD_RES 191 191 Phosphothreonine.
 MOD_RES 259 259 N6-acetyllysine.
 MOD_RES 384 384 Phosphoserine.
 CROSSLNK 449 449 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 577 577 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; Acetylation; Complete proteome; Direct protein sequencing; DNA damage; DNA recombination; DNA repair; DNA replication; DNA-binding; Isopeptide bond; Metal-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Ubl conjugation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 616 AA 
Protein Sequence
MVGQLSEGAI AAIMQKGDTN IKPILQVINI RPITTGNSPP RYRLLMSDGL NTLSSFMLAT 60
QLNPLVEEEQ LSSNCVCQIH RFIVNTLKDG RRVVILMELE VLKSAEAVGV KIGNPVPYNE 120
GLGQPQVAPP APAASPAASS RPQPQNGSSG MGSTVSKAYG ASKTFGKAAG PSLSHTSGGT 180
QSKVVPIASL TPYQSKWTIC ARVTNKSQIR TWSNSRGEGK LFSLELVDES GEIRATAFNE 240
QVDKFFPLIE VNKVYYFSKG TLKIANKQFT AVKNDYEMTF NNETSVMPCE DDHHLPTVQF 300
DFTGIDDLEN KSKDSLVDII GICKSYEDAT KITVRSNNRE VAKRNIYLMD TSGKVVTATL 360
WGEDADKFDG SRQPVLAIKG ARVSDFGGRS LSVLSSSTII ANPDIPEAYK LRGWFDAEGQ 420
ALDGVSISDL KSGGVGGSNT NWKTLYEVKS ENLGQGDKPD YFSSVATVVY LRKENCMYQA 480
CPTQDCNKKV IDQQNGLYRC EKCDTEFPNF KYRMILSVNI ADFQENQWVT CFQESAEAIL 540
GQNAAYLGEL KDKNEQAFEE VFQNANFRSF IFRVRVKVET YNDESRIKAT VMDVKPVDYR 600
EYGRRLVMSI RRSALM 616 
Gene Ontology
 GO:0015629; C:actin cytoskeleton; IDA:HPA.
 GO:0005737; C:cytoplasm; IDA:HPA.
 GO:0005662; C:DNA replication factor A complex; IPI:MGI.
 GO:0000800; C:lateral element; IEA:Compara.
 GO:0001673; C:male germ cell nucleus; IEA:Compara.
 GO:0016605; C:PML body; IDA:MGI.
 GO:0003682; F:chromatin binding; IEA:Compara.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0003697; F:single-stranded DNA binding; TAS:ProtInc.
 GO:0000730; P:DNA recombinase assembly; TAS:Reactome.
 GO:0006271; P:DNA strand elongation involved in DNA replication; TAS:Reactome.
 GO:0000082; P:G1/S transition of mitotic cell cycle; TAS:Reactome.
 GO:0030097; P:hemopoiesis; IEA:Compara.
 GO:0048873; P:homeostasis of number of cells within a tissue; IEA:Compara.
 GO:0001701; P:in utero embryonic development; IEA:Compara.
 GO:0007126; P:meiosis; IEA:Compara.
 GO:0000718; P:nucleotide-excision repair, DNA damage removal; TAS:Reactome.
 GO:0006297; P:nucleotide-excision repair, DNA gap filling; TAS:Reactome.
 GO:0008284; P:positive regulation of cell proliferation; IEA:Compara.
 GO:0000722; P:telomere maintenance via recombination; TAS:Reactome.
 GO:0032201; P:telomere maintenance via semi-conservative replication; TAS:Reactome.
 GO:0006283; P:transcription-coupled nucleotide-excision repair; TAS:Reactome. 
Interpro
 IPR012340; NA-bd_OB-fold.
 IPR004365; NA-bd_OB_tRNA-helicase.
 IPR013955; Rep_factor-A_C.
 IPR007199; Rep_factor-A_N.
 IPR004591; Rep_factor_Rpa1. 
Pfam
 PF04057; Rep-A_N
 PF08646; Rep_fac-A_C
 PF01336; tRNA_anti 
SMART
  
PROSITE
  
PRINTS