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Protein

DNA polymerase delta catalytic subunit

Gene

POLD1

Organism
Bos taurus (Bovine)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Cofactori

[4Fe-4S] clusterBy similarityNote: Binds 1 [4Fe-4S] cluster.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi1011 – 10111ZincBy similarity
Metal bindingi1014 – 10141ZincBy similarity
Metal bindingi1025 – 10251ZincBy similarity
Metal bindingi1028 – 10281ZincBy similarity
Metal bindingi1057 – 10571Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1060 – 10601Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1070 – 10701Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1075 – 10751Iron-sulfur (4Fe-4S)By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1011 – 102818CysA-typeAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

4Fe-4S, DNA-binding, Iron, Iron-sulfur, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase delta catalytic subunit (EC:2.7.7.7)
Gene namesi
Name:POLD1
OrganismiBos taurus (Bovine)
Taxonomic identifieri9913 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos
Proteomesi
  • UP000009136 Componenti: Unplaced

Subcellular locationi

GO - Cellular componenti

  • delta DNA polymerase complex Source: GO_Central
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11061106DNA polymerase delta catalytic subunitPRO_0000046441Add
BLAST

Proteomic databases

PaxDbiP28339.
PRIDEiP28339.

Interactioni

Subunit structurei

Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. The 125 kDa subunit contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity. Interacts with WRNIP1. Interacts with POLD4 and PCNA (By similarity).By similarity

Protein-protein interaction databases

IntActiP28339. 4 interactions.
STRINGi9913.ENSBTAP00000014714.

Structurei

3D structure databases

ProteinModelPortaliP28339.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi4 – 1916Nuclear localization signalSequence analysisAdd
BLAST
Motifi1057 – 107519CysB motifAdd
BLAST

Domaini

The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes.By similarity

Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated
Contains 1 CysA-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1011 – 102818CysA-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0968. Eukaryota.
COG0417. LUCA.
HOVERGENiHBG051395.
InParanoidiP28339.
KOiK02327.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 2 hits.
InterProiIPR006172. 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.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_dom.
IPR025687. Znf-C4pol.
[Graphical view]
PfamiPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
PF14260. zf-C4pol. 1 hit.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P28339-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDGKRRPGPG PGVPPKRARG GLWDEDEAYR PSQFEEELAL MEEMEAERRL
60 70 80 90 100
QEQEEEELQS ALEAADGQFS PTAIDARWLR PAPPALDPQM EPLIFQQLEI
110 120 130 140 150
DHYVAPARPL PGAPPPSQDS VPILRAFGVT NEGVSVCCHI HGFAPYFYTP
160 170 180 190 200
APPGFGPEHL SELQRELSAA ISRDQRGGKE LTGPAVLAVE LCSRESMFGY
210 220 230 240 250
HGHGPSPFLR ITLALPRLMA PARRLLEQGI RLAGLGTPSF APYEANVDFE
260 270 280 290 300
IRFMVDTDIV GCNWLELPAG KYILRPEGKA TLCQLEADVL WSDVISHPPE
310 320 330 340 350
GEWQRIAPLR VLSFDIECAG RKGIFPEPER DPVIQICSLG LRWGEPEPFL
360 370 380 390 400
RLALTLRPCA PILGAKVQSY EREEDLLQAW STFIRIMDPD VITGYNIQNF
410 420 430 440 450
DLPYLISRAQ TLKVPGFPLL GRVIGLRSNI RESSFQSRQT GRRDSKVVSM
460 470 480 490 500
VGRVQMDMLQ VLLREYKLRS YTLNAVSFHF LGEQKEDVQH SIITDLQNGN
510 520 530 540 550
DQTRRRLAVY CLKDAFLPLR LLERLMVLVN AMEMARVTGV PLGYLLSRGQ
560 570 580 590 600
QVKVVSQLLR QAMRQGLLMP VVKTEGGEDY TGATVIEPLK GYYDVPIATL
610 620 630 640 650
DFSSLYPSIM MAHNLCYTTL LRPGAAQKLG LTEDQFIKTP TGDEFVKASV
660 670 680 690 700
RKGLLPQILE NLLSARKRAK AELAKETDPL RRQVLDGRQL ALKVSANSVY
710 720 730 740 750
GFTGAQVGRL PCLEISQSVT GFGRQMIEKT KQLVETKYTV ENGYSTSAKV
760 770 780 790 800
VYGDTDSVMC RFGVSSVAEA MALGREAADW VSGHFPSPIR LEFEKVYFPY
810 820 830 840 850
LLISKKRYAG LLFSSRPDAH DRMDCKGLEA VRRDNCPLVA NLVTASLRRL
860 870 880 890 900
LIDRDPSGAV AHAQDVISDL LCNRIDISQL VITKELTRAA ADYAGKQAHV
910 920 930 940 950
ELAERMRKRD PGSAPSLGDR VPYVIISAAK GVAAYMKSED PLFVLEHSLP
960 970 980 990 1000
IDTQYYLEQQ LAKPLLRIFE PILGEGRAEA VLLRGDHTRC KTVLTGKVGG
1010 1020 1030 1040 1050
LLAFAKRRNC CIGCRTVLSH QGAVCKFCQP RESELYQKEV SHLSALEERF
1060 1070 1080 1090 1100
SRLWTQCQRC QGSLHEDVIC TSRDCPIFYM RKKVRKDLED QERLLRRFGP

PGPEAW
Length:1,106
Mass (Da):123,709
Last modified:December 1, 1992 - v1
Checksum:iEFC2ED155B290431
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M80395 mRNA. Translation: AAA30493.1.
PIRiA39299.
RefSeqiNP_776852.1. NM_174427.2.
UniGeneiBt.4749.

Genome annotation databases

GeneIDi281990.
KEGGibta:281990.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M80395 mRNA. Translation: AAA30493.1.
PIRiA39299.
RefSeqiNP_776852.1. NM_174427.2.
UniGeneiBt.4749.

3D structure databases

ProteinModelPortaliP28339.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP28339. 4 interactions.
STRINGi9913.ENSBTAP00000014714.

Proteomic databases

PaxDbiP28339.
PRIDEiP28339.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi281990.
KEGGibta:281990.

Organism-specific databases

CTDi5424.

Phylogenomic databases

eggNOGiKOG0968. Eukaryota.
COG0417. LUCA.
HOVERGENiHBG051395.
InParanoidiP28339.
KOiK02327.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 2 hits.
InterProiIPR006172. 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.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_dom.
IPR025687. Znf-C4pol.
[Graphical view]
PfamiPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
PF14260. zf-C4pol. 1 hit.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Primary structure of the catalytic subunit of calf thymus DNA polymerase delta: sequence similarities with other DNA polymerases."
    Zhang J., Chung D.W., Tan C.-K., Downey K.M., Davie E.W., So A.G.
    Biochemistry 30:11742-11750(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Identification of a fourth subunit of mammalian DNA polymerase delta."
    Liu L., Mo J.-Y., Rodriguez-Belmonte E.M., Lee M.Y.W.T.
    J. Biol. Chem. 275:18739-18744(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 910-930 AND 968-977, SUBUNIT.
    Tissue: Thymus.

Entry informationi

Entry nameiDPOD1_BOVIN
AccessioniPrimary (citable) accession number: P28339
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: July 6, 2016
This is version 115 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis.

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.