CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-005680
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA polymerase delta catalytic subunit 
Protein Synonyms/Alias
 DNA polymerase subunit delta p125 
Gene Name
 POLD1 
Gene Synonyms/Alias
 POLD 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
272WLELPAGKYALRLKEubiquitination[1]
280YALRLKEKATQCQLEubiquitination[1]
323DIECAGRKGIFPEPEubiquitination[1]
367CAPILGAKVQSYEKEubiquitination[1]
373AKVQSYEKEEDLLQAubiquitination[1, 2]
414ISRAQTLKVQTFPFLubiquitination[1, 2, 3, 4, 5, 6]
439RDSSFQSKQTGRRDTubiquitination[1, 2]
447QTGRRDTKVVSMVGRubiquitination[1, 2]
514RLAVYCLKDAYLPLRubiquitination[1, 5]
554LSRGQQVKVVSQLLRubiquitination[1, 2, 4, 5]
648PTGDEFVKTSVRKGLubiquitination[1, 2, 3, 4, 6]
653FVKTSVRKGLLPQILubiquitination[1, 2, 4]
676RAKAELAKETDPLRRubiquitination[1]
710FTGAQVGKLPCLEISubiquitination[1]
732RQMIEKTKQLVESKYubiquitination[1]
738TKQLVESKYTVENGYubiquitination[1, 2, 3, 4, 6]
750NGYSTSAKVVYGDTDubiquitination[1]
796PIRLEFEKVYFPYLLubiquitination[2, 4]
806FPYLLISKKRYAGLLubiquitination[3]
827AHDRMDCKGLEAVRRubiquitination[4]
885ISQLVITKELTRAASubiquitination[1, 2, 3, 4, 5, 6, 7]
897AASDYAGKQAHVELAubiquitination[1, 2, 4, 6]
909ELAERMRKRDPGSAPubiquitination[1, 2]
998CKTVLTGKVGGLLAFubiquitination[1, 3]
1007GGLLAFAKRRNCCIGacetylation[8]
1007GGLLAFAKRRNCCIGubiquitination[1, 3, 4, 5, 6]
1039RESELYQKEVSHLNAubiquitination[1, 2, 3, 4, 6]
1087YMRKKVRKDLEDQEQubiquitination[1, 2, 3]
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] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [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] 
Functional Description
 Possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. Required with its accessory proteins (proliferating cell nuclear antigen (PCNA) and replication factor C (RFC) or activator 1) for leading strand synthesis. Also involved in completing Okazaki fragments initiated by the DNA polymerase alpha/primase complex. 
Sequence Annotation
 ZN_FING 1012 1029 CysA-type.
 MOTIF 4 19 Nuclear localization signal (Potential).
 MOTIF 1058 1076 CysB motif.
 METAL 1012 1012 Zinc (By similarity).
 METAL 1015 1015 Zinc (By similarity).
 METAL 1026 1026 Zinc (By similarity).
 METAL 1029 1029 Zinc (By similarity).
 METAL 1058 1058 Iron-sulfur (4Fe-4S) (By similarity).
 METAL 1061 1061 Iron-sulfur (4Fe-4S) (By similarity).
 METAL 1071 1071 Iron-sulfur (4Fe-4S) (By similarity).
 METAL 1076 1076 Iron-sulfur (4Fe-4S) (By similarity).  
Keyword
 4Fe-4S; Complete proteome; Disease mutation; DNA replication; DNA-binding; DNA-directed DNA polymerase; Exonuclease; Hydrolase; Iron; Iron-sulfur; Metal-binding; Nuclease; Nucleotidyltransferase; Nucleus; Polymorphism; Reference proteome; Transferase; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1107 AA 
Protein Sequence
MDGKRRPGPG PGVPPKRARG GLWDDDDAPR PSQFEEDLAL MEEMEAEHRL QEQEEEELQS 60
VLEGVADGQV PPSAIDPRWL RPTPPALDPQ TEPLIFQQLE IDHYVGPAQP VPGGPPPSRG 120
SVPVLRAFGV TDEGFSVCCH IHGFAPYFYT PAPPGFGPEH MGDLQRELNL AISRDSRGGR 180
ELTGPAVLAV ELCSRESMFG YHGHGPSPFL RITVALPRLV APARRLLEQG IRVAGLGTPS 240
FAPYEANVDF EIRFMVDTDI VGCNWLELPA GKYALRLKEK ATQCQLEADV LWSDVVSHPP 300
EGPWQRIAPL RVLSFDIECA GRKGIFPEPE RDPVIQICSL GLRWGEPEPF LRLALTLRPC 360
APILGAKVQS YEKEEDLLQA WSTFIRIMDP DVITGYNIQN FDLPYLISRA QTLKVQTFPF 420
LGRVAGLCSN IRDSSFQSKQ TGRRDTKVVS MVGRVQMDML QVLLREYKLR SYTLNAVSFH 480
FLGEQKEDVQ HSIITDLQNG NDQTRRRLAV YCLKDAYLPL RLLERLMVLV NAVEMARVTG 540
VPLSYLLSRG QQVKVVSQLL RQAMHEGLLM PVVKSEGGED YTGATVIEPL KGYYDVPIAT 600
LDFSSLYPSI MMAHNLCYTT LLRPGTAQKL GLTEDQFIRT PTGDEFVKTS VRKGLLPQIL 660
ENLLSARKRA KAELAKETDP LRRQVLDGRQ LALKVSANSV YGFTGAQVGK LPCLEISQSV 720
TGFGRQMIEK TKQLVESKYT VENGYSTSAK VVYGDTDSVM CRFGVSSVAE AMALGREAAD 780
WVSGHFPSPI RLEFEKVYFP YLLISKKRYA GLLFSSRPDA HDRMDCKGLE AVRRDNCPLV 840
ANLVTASLRR LLIDRDPEGA VAHAQDVISD LLCNRIDISQ LVITKELTRA ASDYAGKQAH 900
VELAERMRKR DPGSAPSLGD RVPYVIISAA KGVAAYMKSE DPLFVLEHSL PIDTQYYLEQ 960
QLAKPLLRIF EPILGEGRAE AVLLRGDHTR CKTVLTGKVG GLLAFAKRRN CCIGCRTVLS 1020
HQGAVCEFCQ PRESELYQKE VSHLNALEER FSRLWTQCQR CQGSLHEDVI CTSRDCPIFY 1080
MRKKVRKDLE DQEQLLRRFG PPGPEAW 1107 
Gene Ontology
 GO:0043625; C:delta DNA polymerase complex; IBA:RefGenome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0000109; C:nucleotide-excision repair complex; IDA:UniProtKB.
 GO:0008408; F:3'-5' exonuclease activity; IBA:RefGenome.
 GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
 GO:0003682; F:chromatin binding; IDA:UniProtKB.
 GO:0003677; F:DNA binding; IDA:UniProtKB.
 GO:0003887; F:DNA-directed DNA polymerase activity; IMP:UniProtKB.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0000166; F:nucleotide binding; IEA:InterPro.
 GO:0006287; P:base-excision repair, gap-filling; IDA:UniProtKB.
 GO:0045004; P:DNA replication proofreading; IBA:RefGenome.
 GO:0043137; P:DNA replication, removal of RNA primer; IBA:RefGenome.
 GO:0000731; P:DNA synthesis involved in DNA repair; IDA:UniProtKB.
 GO:0006297; P:nucleotide-excision repair, DNA gap filling; IMP:UniProtKB.
 GO:0007346; P:regulation of mitotic cell cycle; IBA:RefGenome.
 GO:0009411; P:response to UV; TAS:ProtInc.
 GO:0000084; P:S phase of mitotic cell cycle; IDA:UniProtKB.
 GO:0044281; P:small molecule metabolic process; TAS:Reactome.
 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
 IPR006172; DNA-dir_DNA_pol_B.
 IPR017964; DNA-dir_DNA_pol_B_CS.
 IPR006133; DNA-dir_DNA_pol_B_exonuc.
 IPR006134; DNA-dir_DNA_pol_B_multi_dom.
 IPR004578; DNA-dir_DNA_pol_B_pol2.
 IPR023211; DNA_pol_palm_dom.
 IPR012337; RNaseH-like_dom.
 IPR025687; Znf-C4pol. 
Pfam
 PF00136; DNA_pol_B
 PF03104; DNA_pol_B_exo1
 PF14260; zf-C4pol 
SMART
 SM00486; POLBc 
PROSITE
 PS00116; DNA_POLYMERASE_B 
PRINTS
 PR00106; DNAPOLB.