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Protein

DNA polymerase delta catalytic subunit

Gene

DNApol-delta

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed-Annotation score: Annotation score: 4 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

Miscellaneous

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

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)DescriptionActionsGraphical viewLength
Metal bindingi997ZincBy similarity1
Metal bindingi1000ZincBy similarity1
Metal bindingi1014ZincBy similarity1
Metal bindingi1017ZincBy similarity1
Metal bindingi1046Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi1049Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi1059Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi1064Iron-sulfur (4Fe-4S)By similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri997 – 1017CysA-typeAdd BLAST21

GO - Molecular functioni

  • 3'-5'-exodeoxyribonuclease activity Source: FlyBase
  • 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  • DNA binding Source: UniProtKB-KW
  • DNA-directed DNA polymerase activity Source: FlyBase
  • metal ion binding Source: UniProtKB-KW
  • nucleotide binding Source: InterPro

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase
Biological processDNA replication
Ligand4Fe-4S, 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 lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraHolometabolaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 3L

Organism-specific databases

FlyBaseiFBgn0263600. DNApol-delta.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL3124738.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000464471 – 1092DNA polymerase delta catalytic subunitAdd BLAST1092

Proteomic databases

PaxDbiP54358.
PRIDEiP54358.

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 interactors.
DIPiDIP-22360N.
IntActiP54358. 8 interactors.
MINTiMINT-877114.
STRINGi7227.FBpp0075277.

Chemistry databases

BindingDBiP54358.

Structurei

3D structure databases

ProteinModelPortaliP54358.
SMRiP54358.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi4 – 19Nuclear localization signalSequence analysisAdd BLAST16
Motifi1046 – 1064CysB motifAdd BLAST19

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri997 – 1017CysA-typeAdd BLAST21

Keywords - Domaini

Zinc-finger

Phylogenomic databases

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

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 1 hit.
InterProiView protein in 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.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_sf.
IPR036397. RNaseH_sf.
IPR025687. Znf-C4pol.
PfamiView protein in Pfam
PF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
PF14260. zf-C4pol. 1 hit.
PRINTSiPR00106. DNAPOLB.
SMARTiView protein in SMART
SM00486. POLBc. 1 hit.
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiView protein in PROSITE
PS00116. DNA_POLYMERASE_B. 1 hit.

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)DescriptionActionsGraphical viewLength
Sequence conflicti492L → S in CAA61369 (PubMed:8543168).Curated1

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.

Similar proteinsi

Entry informationi

Entry nameiDPOD1_DROME
AccessioniPrimary (citable) accession number: P54358
Secondary accession number(s): Q9VUW8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: February 21, 2001
Last modified: October 25, 2017
This is version 158 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Miscellaneousi

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