CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-006458
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Replication factor C subunit 1 
Protein Synonyms/Alias
 Activator 1 140 kDa subunit; A1 140 kDa subunit; Activator 1 large subunit; Activator 1 subunit 1; DNA-binding protein PO-GA; Replication factor C 140 kDa subunit; RF-C 140 kDa subunit; RFC140; Replication factor C large subunit 
Gene Name
 RFC1 
Gene Synonyms/Alias
 RFC140 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
237AMLDEEPKTKKARKDubiquitination[1, 2]
239LDEEPKTKKARKDTEubiquitination[2]
243PKTKKARKDTEAGETubiquitination[1, 2, 3, 4]
260SVQANLSKAEKHKYPubiquitination[1, 2, 4]
306HSKSSADKIGEVSSPubiquitination[2]
318SSPKASSKLAIMKRKubiquitination[2]
461SGQSKSDKAAALGTKubiquitination[1]
468KAAALGTKIIDEDGLubiquitination[1, 2]
551KETDVFWKSLDFKEQubiquitination[2, 5, 6]
556FWKSLDFKEQVAEETubiquitination[1, 2]
568EETSGDSKARNLADDubiquitination[1]
610GDQSCANKLLRWLRNacetylation[7, 8, 9]
610GDQSCANKLLRWLRNubiquitination[2]
634KHAAKFGKFSGKDDGacetylation[10]
638KFGKFSGKDDGSSFKacetylation[9]
645KDDGSSFKAALLSGPubiquitination[1, 5, 6]
687TRSKSSLKAIVAESLubiquitination[2]
700SLNNTSIKGFYSNGAubiquitination[2]
742QELIGLIKHTKIPIIubiquitination[2, 5, 6, 9]
826SMWCARSKALTYDQAubiquitination[2]
1134SKPSKPEKDKEPRKGubiquitination[4]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [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] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [8] 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]
 [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] 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] 
Functional Description
 The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1. This subunit binds to the primer-template junction. Binds the PO-B transcription element as well as other GA rich DNA sequences. Could play a role in DNA transcription regulation as well as DNA replication and/or repair. Can bind single- or double-stranded DNA. 
Sequence Annotation
 DOMAIN 402 492 BRCT.
 NP_BIND 650 657 ATP (Potential).
 MOTIF 1120 1124 Nuclear localization signal (Potential).
 MOD_RES 67 67 Phosphotyrosine.
 MOD_RES 69 69 Phosphoserine.
 MOD_RES 71 71 Phosphoserine.
 MOD_RES 73 73 Phosphoserine.
 MOD_RES 108 108 Phosphoserine.
 MOD_RES 110 110 Phosphothreonine.
 MOD_RES 156 156 Phosphoserine.
 MOD_RES 161 161 Phosphothreonine.
 MOD_RES 163 163 Phosphothreonine.
 MOD_RES 164 164 Phosphoserine.
 MOD_RES 173 173 Phosphoserine.
 MOD_RES 190 190 Phosphoserine.
 MOD_RES 281 281 Phosphoserine.
 MOD_RES 283 283 Phosphoserine.
 MOD_RES 312 312 Phosphoserine.
 MOD_RES 368 368 Phosphoserine.
 MOD_RES 1104 1104 Phosphoserine.
 MOD_RES 1106 1106 Phosphoserine.  
Keyword
 3D-structure; Activator; Alternative splicing; ATP-binding; Complete proteome; Direct protein sequencing; DNA replication; DNA-binding; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Transcription; Transcription regulation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1148 AA 
Protein Sequence
MDIRKFFGVI PSGKKLVSET VKKNEKTKSD EETLKAKKGI KEIKVNSSRK EDDFKQKQPS 60
KKKRIIYDSD SESEETLQVK NAKKPPEKLP VSSKPGKISR QDPVTYISET DEEDDFMCKK 120
AASKSKENGR STNSHLGTSN MKKNEENTKT KNKPLSPIKL TPTSVLDYFG TGSVQRSNKK 180
MVASKRKELS QNTDESGLND EAIAKQLQLD EDAELERQLH EDEEFARTLA MLDEEPKTKK 240
ARKDTEAGET FSSVQANLSK AEKHKYPHKV KTAQVSDERK SYSPRKQSKY ESSKESQQHS 300
KSSADKIGEV SSPKASSKLA IMKRKEESSY KEIEPVASKR KENAIKLKGE TKTPKKTKSS 360
PAKKESVSPE DSEKKRTNYQ AYRSYLNREG PKALGSKEIP KGAENCLEGL IFVITGVLES 420
IERDEAKSLI ERYGGKVTGN VSKKTNYLVM GRDSGQSKSD KAAALGTKII DEDGLLNLIR 480
TMPGKKSKYE IAVETEMKKE SKLERTPQKN VQGKRKISPS KKESESKKSR PTSKRDSLAK 540
TIKKETDVFW KSLDFKEQVA EETSGDSKAR NLADDSSENK VENLLWVDKY KPTSLKTIIG 600
QQGDQSCANK LLRWLRNWQK SSSEDKKHAA KFGKFSGKDD GSSFKAALLS GPPGVGKTTT 660
ASLVCQELGY SYVELNASDT RSKSSLKAIV AESLNNTSIK GFYSNGAASS VSTKHALIMD 720
EVDGMAGNED RGGIQELIGL IKHTKIPIIC MCNDRNHPKI RSLVHYCFDL RFQRPRVEQI 780
KGAMMSIAFK EGLKIPPPAM NEIILGANQD IRQVLHNLSM WCARSKALTY DQAKADSHRA 840
KKDIKMGPFD VARKVFAAGE ETAHMSLVDK SDLFFHDYSI APLFVQENYI HVKPVAAGGD 900
MKKHLMLLSR AADSICDGDL VDSQIRSKQN WSLLPAQAIY ASVLPGELMR GYMTQFPTFP 960
SWLGKHSSTG KHDRIVQDLA LHMSLRTYSS KRTVNMDYLS LLRDALVQPL TSQGVDGVQD 1020
VVALMDTYYL MKEDFENIME ISSWGGKPSP FSKLDPKVKA AFTRAYNKEA HLTPYSLQAI 1080
KASRHSTSPS LDSEYNEELN EDDSQSDEKD QDAIETDAMI KKKTKSSKPS KPEKDKEPRK 1140
GKGKSSKK 1148 
Gene Ontology
 GO:0005663; C:DNA replication factor C complex; IDA:UniProtKB.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0005524; F:ATP binding; TAS:ProtInc.
 GO:0003689; F:DNA clamp loader activity; IEA:InterPro.
 GO:0008047; F:enzyme activator activity; TAS:ProtInc.
 GO:0006271; P:DNA strand elongation involved in DNA replication; TAS:Reactome.
 GO:0000278; P:mitotic cell cycle; TAS:Reactome.
 GO:0006297; P:nucleotide-excision repair, DNA gap filling; TAS:Reactome.
 GO:0006355; P:regulation of transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0000722; P:telomere maintenance via recombination; TAS:Reactome.
 GO:0032201; P:telomere maintenance via semi-conservative replication; TAS:Reactome.
 GO:0007004; P:telomere maintenance via telomerase; TAS:ProtInc.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0006283; P:transcription-coupled nucleotide-excision repair; TAS:Reactome. 
Interpro
 IPR003593; AAA+_ATPase.
 IPR003959; ATPase_AAA_core.
 IPR001357; BRCT_dom.
 IPR008921; DNA_pol3_clamp-load_cplx_C.
 IPR012178; DNA_replication_fac_C_lsu.
 IPR013725; DNA_replication_fac_RFC1_C.
 IPR027417; P-loop_NTPase. 
Pfam
 PF00004; AAA
 PF00533; BRCT
 PF08519; RFC1 
SMART
 SM00382; AAA
 SM00292; BRCT 
PROSITE
 PS50172; BRCT 
PRINTS