CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-004340
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA polymerase delta catalytic subunit 
Protein Synonyms/Alias
 DNA polymerase III 
Gene Name
 POL3 
Gene Synonyms/Alias
 CDC2; TEX1; YDL102W; D2366 
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
1018SCKGPLRKGEGPLCSubiquitination[1]
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] 
Functional Description
 DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. POL3 contains the polymerase active site and most likely the active site for the 3'- 5' exonuclease activity. 
Sequence Annotation
 ZN_FING 1009 1027 CysA-type.
 MOTIF 1056 1074 CysB motif.
 METAL 1009 1009 Zinc.
 METAL 1012 1012 Zinc.
 METAL 1024 1024 Zinc.
 METAL 1027 1027 Zinc.
 METAL 1056 1056 Iron-sulfur (4Fe-4S).
 METAL 1059 1059 Iron-sulfur (4Fe-4S).
 METAL 1069 1069 Iron-sulfur (4Fe-4S).
 METAL 1074 1074 Iron-sulfur (4Fe-4S).
 MOD_RES 30 30 Phosphoserine.
 MOD_RES 37 37 Phosphoserine.
 MOD_RES 56 56 Phosphoserine; by ATM or ATR.  
Keyword
 3D-structure; 4Fe-4S; Complete proteome; DNA replication; DNA-binding; DNA-directed DNA polymerase; Exonuclease; Hydrolase; Iron; Iron-sulfur; Metal-binding; Nuclease; Nucleotidyltransferase; Nucleus; Phosphoprotein; Reference proteome; Transferase; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1097 AA 
Protein Sequence
MSEKRSLPMV DVKIDDEDTP QLEKKIKRQS IDHGVGSEPV STIEIIPSDS FRKYNSQGFK 60
AKDTDLMGTQ LESTFEQELS QMEHDMADQE EHDLSSFERK KLPTDFDPSL YDISFQQIDA 120
EQSVLNGIKD ENTSTVVRFF GVTSEGHSVL CNVTGFKNYL YVPAPNSSDA NDQEQINKFV 180
HYLNETFDHA IDSIEVVSKQ SIWGYSGDTK LPFWKIYVTY PHMVNKLRTA FERGHLSFNS 240
WFSNGTTTYD NIAYTLRLMV DCGIVGMSWI TLPKGKYSMI EPNNRVSSCQ LEVSINYRNL 300
IAHPAEGDWS HTAPLRIMSF DIECAGRIGV FPEPEYDPVI QIANVVSIAG AKKPFIRNVF 360
TLNTCSPITG SMIFSHATEE EMLSNWRNFI IKVDPDVIIG YNTTNFDIPY LLNRAKALKV 420
NDFPYFGRLK TVKQEIKESV FSSKAYGTRE TKNVNIDGRL QLDLLQFIQR EYKLRSYTLN 480
AVSAHFLGEQ KEDVHYSIIS DLQNGDSETR RRLAVYCLKD AYLPLRLMEK LMALVNYTEM 540
ARVTGVPFSY LLARGQQIKV VSQLFRKCLE IDTVIPNMQS QASDDQYEGA TVIEPIRGYY 600
DVPIATLDFN SLYPSIMMAH NLCYTTLCNK ATVERLNLKI DEDYVITPNG DYFVTTKRRR 660
GILPIILDEL ISARKRAKKD LRDEKDPFKR DVLNGRQLAL KISANSVYGF TGATVGKLPC 720
LAISSSVTAY GRTMILKTKT AVQEKYCIKN GYKHDAVVVY GDTDSVMVKF GTTDLKEAMD 780
LGTEAAKYVS TLFKHPINLE FEKAYFPYLL INKKRYAGLF WTNPDKFDKL DQKGLASVRR 840
DSCSLVSIVM NKVLKKILIE RNVDGALAFV RETINDILHN RVDISKLIIS KTLAPNYTNP 900
QPHAVLAERM KRREGVGPNV GDRVDYVIIG GNDKLYNRAE DPLFVLENNI QVDSRYYLTN 960
QLQNPIISIV APIIGDKQAN GMFVVKSIKI NTGSQKGGLM SFIKKVEACK SCKGPLRKGE 1020
GPLCSNCLAR SGELYIKALY DVRDLEEKYS RLWTQCQRCA GNLHSEVLCS NKNCDIFYMR 1080
VKVKKELQEK VEQLSKW 1097 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0043625; C:delta DNA polymerase complex; IBA:RefGenome.
 GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0003887; F:DNA-directed DNA polymerase activity; IDA:SGD.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0000166; F:nucleotide binding; IEA:InterPro.
 GO:0008310; F:single-stranded DNA specific 3'-5' exodeoxyribonuclease activity; TAS:SGD.
 GO:0006287; P:base-excision repair, gap-filling; IBA:RefGenome.
 GO:0045004; P:DNA replication proofreading; IBA:RefGenome.
 GO:0043137; P:DNA replication, removal of RNA primer; IDA:SGD.
 GO:0006297; P:nucleotide-excision repair, DNA gap filling; IBA:RefGenome.
 GO:0007346; P:regulation of mitotic cell cycle; IBA:RefGenome.
 GO:0006278; P:RNA-dependent DNA replication; IDA:SGD. 
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.