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Protein

DNA polymerase delta catalytic subunit

Gene

DNApol-delta

Organism
Drosophila melanogaster (Fruit fly)
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 bindingi997 – 9971ZincBy similarity
Metal bindingi1000 – 10001ZincBy similarity
Metal bindingi1014 – 10141ZincBy similarity
Metal bindingi1017 – 10171ZincBy similarity
Metal bindingi1046 – 10461Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1049 – 10491Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1059 – 10591Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1064 – 10641Iron-sulfur (4Fe-4S)By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri997 – 101721CysA-typeAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • base-excision repair, gap-filling Source: GO_Central
  • cellular response to DNA damage stimulus Source: FlyBase
  • DNA replication proofreading Source: GO_Central
  • lagging strand elongation Source: FlyBase
  • leading strand elongation Source: FlyBase
  • neurogenesis Source: FlyBase
  • nucleotide-excision repair, DNA gap filling Source: GO_Central
  • sensory perception of pain Source: FlyBase
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

Enzyme and pathway databases

ReactomeiR-DME-69166. Removal of the Flap Intermediate.
R-DME-69183. Processive synthesis on the lagging strand.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase delta catalytic subunit (EC:2.7.7.7)
Gene namesi
Name:DNApol-delta
Synonyms:POLD
ORF Names:CG5949
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 3L

Organism-specific databases

FlyBaseiFBgn0263600. DNApol-delta.

Subcellular locationi

GO - Cellular componenti

  • delta DNA polymerase complex Source: FlyBase
  • microtubule associated complex Source: FlyBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL3124738.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10921092DNA polymerase delta catalytic subunitPRO_0000046447Add
BLAST

Proteomic databases

PaxDbiP54358.

Expressioni

Gene expression databases

BgeeiFBgn0263600.
GenevisibleiP54358. DM.

Interactioni

Subunit structurei

Heterodimer with subunits of 125 kDa and 50 kDa. The 125 kDa subunit contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity (By similarity).By similarity

Protein-protein interaction databases

BioGridi65057. 13 interactions.
DIPiDIP-22360N.
IntActiP54358. 8 interactions.
MINTiMINT-877114.
STRINGi7227.FBpp0075277.

Chemistry

BindingDBiP54358.

Structurei

3D structure databases

ProteinModelPortaliP54358.
SMRiP54358. Positions 66-962.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi4 – 1916Nuclear localization signalSequence analysisAdd
BLAST
Motifi1046 – 106419CysB 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 fingeri997 – 101721CysA-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0968. Eukaryota.
COG0417. LUCA.
GeneTreeiENSGT00560000077365.
InParanoidiP54358.
KOiK02327.
OMAiEQASLCP.
OrthoDBiEOG091G00TM.
PhylomeDBiP54358.

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.

P54358-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDGKRKFNGT SNGHAKKPRN PDDDEEMGFE AELAAFENSE DMDQTLLMGD
60 70 80 90 100
GPENQTTSER WSRPPPPELD PSKHNLEFQQ LDVENYLGQP LPGMPGAQIG
110 120 130 140 150
PVPVVRMFGV TMEGNSVCCH VHGFCPYFYI EAPSQFEEHH CEKLQKALDQ
160 170 180 190 200
KVIADIRNNK DNVQEAVLMV ELVEKLNIHG YNGDKKQRYI KISVTLPRFV
210 220 230 240 250
AAASRLLKKE VIMSEIDFQD CRAFENNIDF DIRFMVDTDV VGCNWIELPM
260 270 280 290 300
GHWRIRNSHS KPLPESRCQI EVDVAFDRFI SHEPEGEWSK VAPFRILSFD
310 320 330 340 350
IECAGRKGIF PEAKIDPVIQ IANMVIRQGE REPFIRNVFT LNECAPIIGS
360 370 380 390 400
QVLCHDKETQ MLDKWSAFVR EVDPDILTGY NINNFDFPYL LNRAAHLKVR
410 420 430 440 450
NFEYLGRIKN IRSVIKEQML QSKQMGRREN QYVNFEGRVP FDLLFVLLRD
460 470 480 490 500
YKLRSYTLNA VSYHFLQEQK EDVHHSIITD LQNGDEQTRR RLAMYCLKDA
510 520 530 540 550
YLPLRLLEKL MAIVNYMEMA RVTGVPLESL LTRGQQIKVL SQLLRKAKTK
560 570 580 590 600
GFIMPSYTSQ GSDEQYEGAT VIEPKRGYYA DPISTLDFAS LYPSIMMAHN
610 620 630 640 650
LCYTTLVLGG TREKLRQQEN LQDDQVERTP ANNYFVKSEV RRGLLPEILE
660 670 680 690 700
SLLAARKRAK NDLKVETDPF KRKVLDGRQL ALKISANSVY GFTGAQVGKL
710 720 730 740 750
PCLEISGSVT AYGRTMIEMT KNEVESHYTQ ANGYENNAVV IYGDTDSVMV
760 770 780 790 800
NFGVKTLERS MELGREAAEL VSSKFVHPIK LEFEKVYYPY LLINKKRYAG
810 820 830 840 850
LYFTRPDTYD KMDCKGIETV RRDNSPLVAN LMNSCLQKLL IERDPDGAVA
860 870 880 890 900
YVKQVIADLL CNRIDISHLV ITKELAKTDY AAKQAHVELA AKMKKRDPGT
910 920 930 940 950
APKLGDRVPY VICAAAKNTP AYQKAEDPLY VLENSVPIDA TYYLEQQLSK
960 970 980 990 1000
PLLRIFEPIL GDNAESILLK GEHTRTRTVV TSKVGGLAGF MTKKTSCLGC
1010 1020 1030 1040 1050
KSLMPKGYEQ ACLCPHCEPR MSELYQKEVG AKRELEETFS RLWTECQRCQ
1060 1070 1080 1090
ESLHEEVICS NRDCPIFYMR QKVRMDLDNQ EKRVLRFGLA EW
Length:1,092
Mass (Da):124,905
Last modified:February 21, 2001 - v2
Checksum:i2FA380420298EA5C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti492 – 4921L → S in CAA61369 (PubMed:8543168).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X88928 mRNA. Translation: CAA61369.1.
AE014296 Genomic DNA. Translation: AAF49555.1.
AY113526 mRNA. Translation: AAM29531.1.
RefSeqiNP_524099.2. NM_079375.3.
UniGeneiDm.2838.

Genome annotation databases

EnsemblMetazoaiFBtr0075522; FBpp0075277; FBgn0263600.
GeneIDi39746.
KEGGidme:Dmel_CG5949.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X88928 mRNA. Translation: CAA61369.1.
AE014296 Genomic DNA. Translation: AAF49555.1.
AY113526 mRNA. Translation: AAM29531.1.
RefSeqiNP_524099.2. NM_079375.3.
UniGeneiDm.2838.

3D structure databases

ProteinModelPortaliP54358.
SMRiP54358. Positions 66-962.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi65057. 13 interactions.
DIPiDIP-22360N.
IntActiP54358. 8 interactions.
MINTiMINT-877114.
STRINGi7227.FBpp0075277.

Chemistry

BindingDBiP54358.
ChEMBLiCHEMBL3124738.

Proteomic databases

PaxDbiP54358.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0075522; FBpp0075277; FBgn0263600.
GeneIDi39746.
KEGGidme:Dmel_CG5949.

Organism-specific databases

CTDi39746.
FlyBaseiFBgn0263600. DNApol-delta.

Phylogenomic databases

eggNOGiKOG0968. Eukaryota.
COG0417. LUCA.
GeneTreeiENSGT00560000077365.
InParanoidiP54358.
KOiK02327.
OMAiEQASLCP.
OrthoDBiEOG091G00TM.
PhylomeDBiP54358.

Enzyme and pathway databases

ReactomeiR-DME-69166. Removal of the Flap Intermediate.
R-DME-69183. Processive synthesis on the lagging strand.

Miscellaneous databases

GenomeRNAii39746.
PROiP54358.

Gene expression databases

BgeeiFBgn0263600.
GenevisibleiP54358. DM.

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...

Entry informationi

Entry nameiDPOD1_DROME
AccessioniPrimary (citable) accession number: P54358
Secondary accession number(s): Q9VUW8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: February 21, 2001
Last modified: September 7, 2016
This is version 148 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

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. Drosophila
    Drosophila: entries, gene names and cross-references to FlyBase
  2. 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.