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Protein

DNA polymerase delta catalytic subunit

Gene

pol3

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.

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 bindingi993ZincBy similarity1
Metal bindingi996ZincBy similarity1
Metal bindingi1008ZincBy similarity1
Metal bindingi1011ZincBy similarity1
Metal bindingi1040Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi1043Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi1053Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi1058Iron-sulfur (4Fe-4S)By similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri993 – 1011CysA-typeAdd BLAST19

GO - Molecular functioni

GO - Biological processi

  • base-excision repair, gap-filling Source: GO_Central
  • DNA replication proofreading Source: GO_Central
  • DNA strand elongation involved in DNA replication Source: PomBase
  • DNA synthesis involved in UV-damage excision repair Source: PomBase
  • mitotic DNA replication lagging strand elongation Source: PomBase
  • nucleotide-excision repair, DNA gap filling Source: GO_Central

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-SPO-110314 Recognition of DNA damage by PCNA-containing replication complex
R-SPO-174411 Polymerase switching on the C-strand of the telomere
R-SPO-174414 Processive synthesis on the C-strand of the telomere
R-SPO-174417 Telomere C-strand (Lagging Strand) Synthesis
R-SPO-174437 Removal of the Flap Intermediate from the C-strand
R-SPO-5651801 PCNA-Dependent Long Patch Base Excision Repair
R-SPO-5656169 Termination of translesion DNA synthesis
R-SPO-5696397 Gap-filling DNA repair synthesis and ligation in GG-NER
R-SPO-5696400 Dual Incision in GG-NER
R-SPO-6782135 Dual incision in TC-NER
R-SPO-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SPO-69091 Polymerase switching
R-SPO-69166 Removal of the Flap Intermediate
R-SPO-69183 Processive synthesis on the lagging strand

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase delta catalytic subunit (EC:2.7.7.7)
Alternative name(s):
DNA polymerase III
Gene namesi
Name:pol3
Synonyms:pold
ORF Names:SPBC336.04
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC336.04
PomBaseiSPBC336.04

Subcellular locationi

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

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000464531 – 1086DNA polymerase delta catalytic subunitAdd BLAST1086

Proteomic databases

MaxQBiP30316
PaxDbiP30316
PRIDEiP30316

PTM databases

iPTMnetiP30316

Interactioni

Subunit structurei

Heterotetramer that consist of the pol3, cdc1, cdc27 and cdm1 subunits. The pol3 subunit contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity.

Binary interactionsi

WithEntry#Exp.IntActNotes
cdc1P873242EBI-865207,EBI-865227

Protein-protein interaction databases

BioGridi276786, 34 interactors
ComplexPortaliCPX-2100 DNA polymerase delta heterotetramer
IntActiP30316, 1 interactor
STRINGi4896.SPBC336.04.1

Structurei

3D structure databases

ProteinModelPortaliP30316
SMRiP30316
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1040 – 1058CysB 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 fingeri993 – 1011CysA-typeAdd BLAST19

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOGENOMiHOG000036616
InParanoidiP30316
KOiK02327
OMAiCLVNYTE
OrthoDBiEOG092C0BQT
PhylomeDBiP30316

Family and domain databases

Gene3Di3.30.420.10, 1 hit
3.90.1600.10, 2 hits
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_sf
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.

P30316-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTDRSSNEGV VLNKENYPFP RRNGSIHGEI TDVKRRRLSE RNGYGDKKGS
60 70 80 90 100
SSKEKTSSFE DELAEYASQL DQDEIKSSKD QQWQRPALPA INPEKDDIYF
110 120 130 140 150
QQIDSEEFTE GSVPSIRLFG VTDNGNSILV HVVGFLPYFY VKAPVGFRPE
160 170 180 190 200
MLERFTQDLD ATCNGGVIDH CIIEMKENLY GFQGNEKSPF IKIFTTNPRI
210 220 230 240 250
LSRARNVFER GEFNFEELFP VGVGVTTFES NTQYLLRFMI DCDVVGMNWI
260 270 280 290 300
HLPASKYQFR YQNRVSNCQI EAWINYKDLI SLPAEGQWSK MAPLRIMSFD
310 320 330 340 350
IECAGRKGVF PDPSIDPVIQ IASIVTQYGD STPFVRNVFC VDTCSQIVGT
360 370 380 390 400
QVYEFQNQAE MLSSWSKFVR DVDPDVLIGY NICNFDIPYL LDRAKSLRIH
410 420 430 440 450
NFPLLGRIHN FFSVAKETTF SSKAYGTRES KTTSIPGRLQ LDMLQVMQRD
460 470 480 490 500
FKLRSYSLNA VCSQFLGEQK EDVHYSIITD LQNGTADSRR RLAIYCLKDA
510 520 530 540 550
YLPQRLMDKL MCFVNYTEMA RVTGVPFNFL LARGQQIKVI SQLFRKALQH
560 570 580 590 600
DLVVPNIRVN GTDEQYEGAT VIEPIKGYYD TPIATLDFSS LYPSIMQAHN
610 620 630 640 650
LCYTTLLDSN TAELLKLKQD VDYSVTPNGD YFVKPHVRKG LLPIILADLL
660 670 680 690 700
NARKKAKADL KKETDPFKKA VLDGRQLALK VSANSVYGFT GATNGRLPCL
710 720 730 740 750
AISSSVTSYG RQMIEKTKDV VEKRYRIENG YSHDAVVIYG DTDSVMVKFG
760 770 780 790 800
VKTLPEAMKL GEEAANYVSD QFPNPIKLEF EKVYFPYLLI SKKRYAGLFW
810 820 830 840 850
TRTDTYDKMD SKGIETVRRD NCPLVSYVID TALRKMLIDQ DVEGAQLFTK
860 870 880 890 900
KVISDLLQNK IDMSQLVITK ALSKTDYAAK MAHVELAERM RKRDAGSAPA
910 920 930 940 950
IGDRVAYVII KGAQGDQFYM RSEDPIYVLE NNIPIDAKYY LENQLSKPLL
960 970 980 990 1000
RIFEPILGEK ASSLLHGDHT RTISMAAPSV GGIMKFAVKV ETCLGCKAPI
1010 1020 1030 1040 1050
KKGKTALCEN CLNRSAELYQ RQVAQVNDLE VRFARLWTQC QRCQGSMHQD
1060 1070 1080
VICTSRDCPI FYMRIAEHKK LQQSVDLLKR FDEMSW
Length:1,086
Mass (Da):123,569
Last modified:January 11, 2001 - v2
Checksum:i99F528413220C3CA
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti102Q → E in CAA41968 (PubMed:1960723).Curated1
Sequence conflicti290K → Q in BAA87100 (PubMed:10759889).Curated1
Sequence conflicti419T → S in CAA41968 (PubMed:1960723).Curated1
Sequence conflicti545R → C in CAA41968 (PubMed:1960723).Curated1
Sequence conflicti545R → C in AAA35303 (PubMed:8443413).Curated1
Sequence conflicti777 – 784KLEFEKVY → NWSFST in CAA41968 (PubMed:1960723).Curated8
Sequence conflicti866L → H in CAA41968 (PubMed:1960723).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X59278 Genomic DNA Translation: CAA41968.1
L07734 Genomic DNA Translation: AAA35303.1
CU329671 Genomic DNA Translation: CAB58156.1
AB027796 Genomic DNA Translation: BAA87100.1
PIRiS19661
T40242
T43266
RefSeqiNP_596124.1, NM_001022042.2

Genome annotation databases

EnsemblFungiiSPBC336.04.1; SPBC336.04.1:pep; SPBC336.04
GeneIDi2540255
KEGGispo:SPBC336.04

Similar proteinsi

Entry informationi

Entry nameiDPOD_SCHPO
AccessioniPrimary (citable) accession number: P30316
Secondary accession number(s): Q10016, Q9USU0, Q9UU61
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: January 11, 2001
Last modified: June 20, 2018
This is version 169 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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