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Protein

DNA polymerase delta catalytic subunit

Gene

Pold1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript 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 (By similarity).By similarity

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 bindingi1008 – 10081ZincBy similarity
Metal bindingi1011 – 10111ZincBy similarity
Metal bindingi1022 – 10221ZincBy similarity
Metal bindingi1025 – 10251ZincBy similarity
Metal bindingi1054 – 10541Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1057 – 10571Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1067 – 10671Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1072 – 10721Iron-sulfur (4Fe-4S)By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1008 – 102518CysA-typeAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • base-excision repair, gap-filling Source: GO_Central
  • cellular response to UV Source: UniProtKB
  • DNA biosynthetic process Source: RGD
  • DNA-dependent DNA replication Source: RGD
  • DNA replication Source: RGD
  • DNA replication proofreading Source: GO_Central
  • fatty acid homeostasis Source: UniProtKB
  • nucleotide-excision repair, DNA gap filling Source: GO_Central
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
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi621839. Pold1.

Subcellular locationi

GO - Cellular componenti

  • delta DNA polymerase complex Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11031103DNA polymerase delta catalytic subunitPRO_0000046445Add
BLAST

Proteomic databases

PaxDbiO54747.
PRIDEiO54747.

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

STRINGi10116.ENSRNOP00000026797.

Structurei

3D structure databases

ProteinModelPortaliO54747.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi4 – 1714Nuclear localization signalSequence analysisAdd
BLAST
Motifi1054 – 107219CysB 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 fingeri1008 – 102518CysA-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0968. Eukaryota.
COG0417. LUCA.
HOGENOMiHOG000036616.
HOVERGENiHBG051395.
InParanoidiO54747.
KOiK02327.
PhylomeDBiO54747.

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.

O54747-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDGKRRQAPS SGVPPKRACK GLWDEDEPSQ FEENLALLEE IEAENRLQEA
60 70 80 90 100
EEELQLPPEG IVGGQFSTAD IDPRWLRPTP LALDPSTEPL IFQQLEIDHY
110 120 130 140 150
VGTSPPLPEG PPASRNSVPI LRAFGVTDEG FSVCCHIHGF APYFYTPAPP
160 170 180 190 200
GFGAEHLSEL QRELNAAISR DQRGGKELSG PAVLAIELCS RESMFGYHGH
210 220 230 240 250
GPSPFLRITL ALPRLMAPAR RLLEQGIRVP GLGTPSFAPY EANVDFEIRF
260 270 280 290 300
MVDADIVGCN WLELPAGKYV RRAEKKATLC QLEVDVLWSD VISHPPEGQW
310 320 330 340 350
QRIAPLRVLS FDIECAGRKG IFPEPERDPV IQICSLGLRW GEPEPFLRLA
360 370 380 390 400
LTLRPCAPIL GAKVQSYERE EDLLQAWATF ILAMDPDVIT GYNIQNFDLP
410 420 430 440 450
YLISRAQTLK VDRFPFLGRV TGLRSNIRDS SFQSRQVGRR DSKVVSMVGR
460 470 480 490 500
VQMDMLQVLL REYKLRSYTL NAVSFHFLGE QKEDVQHSII TDLQNGNEQT
510 520 530 540 550
RRRLAVYCLK DAFLPLRLLE RLMVLVNNVE MARVTGVPLG YLLSRGQQVK
560 570 580 590 600
VVSQLLRQAM REGLLMPVVK TEGGEDYTGA TVIEPLKGYY DVPIATLDFS
610 620 630 640 650
SLYPSIMMAH NLCYTTLLRP GAAQKLGLKP DEFIKTPTGD EFVKASVRKG
660 670 680 690 700
LLPQILENLL SARKRAKAEL AQETDPLRRQ VLDGRQLALK VSPNSVYGFT
710 720 730 740 750
GAQVGKLPCL EISQSVTGFG RQMIEKTKQL VETKYTLENG YDANAKVVYG
760 770 780 790 800
DTDSVMCRFG VSSVAEAMSL GREAANWVSS HFPSPIRLEF EKVYFPYLLI
810 820 830 840 850
SKKRYAGLLF SSRSDAHDRM DCKGLEAVRR DNCPLVANLV TSSLRRILVD
860 870 880 890 900
RDPDGAVAHA KDVISDLLCN RIDISQLVIT KELTRAAADY AGKQAHVELA
910 920 930 940 950
ERMRKRDPGS APNLGDRVPY VIIGAAKGVA AYMKSEDPLF VLEHSLPIDT
960 970 980 990 1000
QYYLEQQLAK PLLRIFEPIL GEGRAESVLL RGDHTRCKTV LTSKVGGLLA
1010 1020 1030 1040 1050
FTKRRNSCIG CRSVIDHQGA VCKFCQPRES ELYQKEVSHL NALEERFSRL
1060 1070 1080 1090 1100
WTQCQRCQGS LHEDVICTSR DCPIFYMRKK VRKDLEDQER LLQRFGPPGP

EAW
Length:1,103
Mass (Da):123,601
Last modified:June 1, 1998 - v1
Checksum:i361086DDC1B50639
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ222691 mRNA. Translation: CAA10946.1.
RefSeqiNP_067694.1. NM_021662.2.
UniGeneiRn.88690.

Genome annotation databases

GeneIDi59294.
KEGGirno:59294.
UCSCiRGD:621839. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ222691 mRNA. Translation: CAA10946.1.
RefSeqiNP_067694.1. NM_021662.2.
UniGeneiRn.88690.

3D structure databases

ProteinModelPortaliO54747.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000026797.

Proteomic databases

PaxDbiO54747.
PRIDEiO54747.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi59294.
KEGGirno:59294.
UCSCiRGD:621839. rat.

Organism-specific databases

CTDi5424.
RGDi621839. Pold1.

Phylogenomic databases

eggNOGiKOG0968. Eukaryota.
COG0417. LUCA.
HOGENOMiHOG000036616.
HOVERGENiHBG051395.
InParanoidiO54747.
KOiK02327.
PhylomeDBiO54747.

Miscellaneous databases

PROiO54747.

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. "Evidence for reduced copying fidelity of DNA polymerases alpha, delta, and epsilon from Novikoff hepatoma cells."
    Fox G., Popanda O., Thielmann H.W.
    J. Cancer Res. Clin. Oncol. 123:659-668(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Sprague-Dawley.
    Tissue: Liver.

Entry informationi

Entry nameiDPOD1_RAT
AccessioniPrimary (citable) accession number: O54747
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: June 1, 1998
Last modified: July 6, 2016
This is version 116 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, 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.