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Protein

DNA polymerase delta catalytic subunit

Gene

F10C2.4

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 bindingi981 – 9811ZincBy similarity
Metal bindingi984 – 9841ZincBy similarity
Metal bindingi998 – 9981ZincBy similarity
Metal bindingi1001 – 10011ZincBy similarity
Metal bindingi1030 – 10301Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1033 – 10331Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1043 – 10431Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1048 – 10481Iron-sulfur (4Fe-4S)By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri981 – 100121CysA-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

Enzyme and pathway databases

ReactomeiR-CEL-69166. Removal of the Flap Intermediate.
R-CEL-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
ORF Names:F10C2.4
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome V

Organism-specific databases

WormBaseiF10C2.4; CE09308; WBGene00008645.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10811081DNA polymerase delta catalytic subunitPRO_0000046446Add
BLAST

Proteomic databases

EPDiP90829.
PaxDbiP90829.
PRIDEiP90829.

PTM databases

iPTMnetiP90829.

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

STRINGi6239.F10C2.4.

Structurei

3D structure databases

ProteinModelPortaliP90829.
SMRiP90829. Positions 211-951.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1030 – 104819CysB 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 fingeri981 – 100121CysA-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0968. Eukaryota.
COG0417. LUCA.
GeneTreeiENSGT00560000077365.
HOGENOMiHOG000036616.
InParanoidiP90829.
KOiK02327.
OMAiRQAMKQD.
OrthoDBiEOG7992PP.
PhylomeDBiP90829.

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.

P90829-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSKRPGGSS FQPEVKRKRE SDEFEQCYVS RFENELPSVP TIDKTGWARP
60 70 80 90 100
AVDKDLGISK SIACQILEVE TYHEDGSATS YDRTNVKLYG VTKSGNSICV
110 120 130 140 150
IVTDYFPHFY FQAPQGFGVE HIGTAQSAIC NMVAAAKRRG GSGQAQLPGK
160 170 180 190 200
VVDNLVHVEI VHGENLYYFR GADTKVPFVK VSGSTEALHK ARMELKNGVN
210 220 230 240 250
LMGKGPVNVG NLYESNINVI VMFLAKTNIV GCGWIEIPAG KCRILSNSEK
260 270 280 290 300
SSRCQIEVTV PVKNLIVHES DGEWAGIAPI RTLSLDIECI GRRGVFPEAI
310 320 330 340 350
KDPIIQIANL VKIEGEAEPF VRNCFVLGTC APVVGSNIIQ CVNEKVLLEK
360 370 380 390 400
WAEFVREVDP DIITGYNILN FDLPYILDRA KVLSLPQVSH LGRQKEKGSV
410 420 430 440 450
VRDAAISSKQ MGSRVNKSID IHGRIIFDVL QVVLRDYKLR SYTLNSVSYQ
460 470 480 490 500
FLSEQKEDVE HNIIPDLQRG DEQTRRRLAQ YCLKDAYLPL RLLDKLMSII
510 520 530 540 550
NYIEMARVTG VPMNFLLTKG QQIKILSMML RRCKQNNFFL PVIEANSGDG
560 570 580 590 600
EGYEGATVID PIRGFYNEPI ATLDFASLYP SIMIAHNLCY TTLLKSPQGV
610 620 630 640 650
ENEDYIRTPS GQYFATKSKR RGLLPEILED ILAARKRAKN DMKNEKDEFK
660 670 680 690 700
RMVYNGRQLA LKISANSVYG FTGATVGKLP CLEISQSVTA FGRKMIDMTK
710 720 730 740 750
LEVERIYKKG ALDGKCPADA KVIYGDTDSV MVKFGVETVA QAMEIGLDAA
760 770 780 790 800
KEVSKIFTPP IKLEFEKVYS PYLLINKKRY AGLYFTKPDV HDKMDCKGLE
810 820 830 840 850
TVRRDNCPLV AKVLGVCLEK LLIERDQQSA LDFAKRTISD LLCNKIDISL
860 870 880 890 900
LIISKELTKS GDKYQAKQAH VELAARMKKR DAGSAPRLGD RVPYVFVAAA
910 920 930 940 950
KNVPAYERAE DPTFVLQNNI PLDTKHYLTN QLAKPLARIF EPILGDRAEK
960 970 980 990 1000
ILVEGEHTRV RTVVQSKVGG LAAFTTKSAT CLGCKSVLPR AESENAVCKH
1010 1020 1030 1040 1050
CEPKLPTIFA SRMNTMHELE NHFGRLWTEC QNCAKTMQDK VNCSARDCPI
1060 1070 1080
YYMREKVRNE LSEASAVIER FGDPCFQAPT K
Length:1,081
Mass (Da):120,830
Last modified:May 1, 1997 - v1
Checksum:i405954DDCC61F07E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z81497 Genomic DNA. Translation: CAB04077.1.
PIRiT20698.
RefSeqiNP_506017.1. NM_073616.3.
UniGeneiCel.5663.

Genome annotation databases

EnsemblMetazoaiF10C2.4; F10C2.4; WBGene00008645.
GeneIDi179652.
KEGGicel:CELE_F10C2.4.
UCSCiF10C2.4. c. elegans.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z81497 Genomic DNA. Translation: CAB04077.1.
PIRiT20698.
RefSeqiNP_506017.1. NM_073616.3.
UniGeneiCel.5663.

3D structure databases

ProteinModelPortaliP90829.
SMRiP90829. Positions 211-951.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi6239.F10C2.4.

PTM databases

iPTMnetiP90829.

Proteomic databases

EPDiP90829.
PaxDbiP90829.
PRIDEiP90829.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiF10C2.4; F10C2.4; WBGene00008645.
GeneIDi179652.
KEGGicel:CELE_F10C2.4.
UCSCiF10C2.4. c. elegans.

Organism-specific databases

CTDi179652.
WormBaseiF10C2.4; CE09308; WBGene00008645.

Phylogenomic databases

eggNOGiKOG0968. Eukaryota.
COG0417. LUCA.
GeneTreeiENSGT00560000077365.
HOGENOMiHOG000036616.
InParanoidiP90829.
KOiK02327.
OMAiRQAMKQD.
OrthoDBiEOG7992PP.
PhylomeDBiP90829.

Enzyme and pathway databases

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

Miscellaneous databases

PROiP90829.

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. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bristol N2.

Entry informationi

Entry nameiDPOD1_CAEEL
AccessioniPrimary (citable) accession number: P90829
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 21, 2001
Last sequence update: May 1, 1997
Last modified: June 8, 2016
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis 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. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  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.