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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: Annotation score: 5 out of 5-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.

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 bindingi993 – 9931ZincBy similarity
Metal bindingi996 – 9961ZincBy similarity
Metal bindingi1008 – 10081ZincBy similarity
Metal bindingi1011 – 10111ZincBy similarity
Metal bindingi1040 – 10401Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1043 – 10431Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1053 – 10531Iron-sulfur (4Fe-4S)By similarity
Metal bindingi1058 – 10581Iron-sulfur (4Fe-4S)By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri993 – 101119CysA-typeAdd
BLAST

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
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-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-69109. Leading Strand Synthesis.
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

GO - Cellular componenti

  • delta DNA polymerase complex Source: PomBase
  • nuclear chromosome, telomeric region Source: PomBase
  • nuclear replication fork Source: PomBase
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10861086DNA polymerase delta catalytic subunitPRO_0000046453Add
BLAST

Proteomic databases

MaxQBiP30316.

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. 33 interactions.
IntActiP30316. 1 interaction.
MINTiMINT-4688192.

Structurei

3D structure databases

ProteinModelPortaliP30316.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1040 – 105819CysB 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 fingeri993 – 101119CysA-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOGENOMiHOG000036616.
InParanoidiP30316.
KOiK02327.
OMAiEQASLCP.
OrthoDBiEOG092C0BQT.
PhylomeDBiP30316.

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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti102 – 1021Q → E in CAA41968 (PubMed:1960723).Curated
Sequence conflicti290 – 2901K → Q in BAA87100 (PubMed:10759889).Curated
Sequence conflicti419 – 4191T → S in CAA41968 (PubMed:1960723).Curated
Sequence conflicti545 – 5451R → C in CAA41968 (PubMed:1960723).Curated
Sequence conflicti545 – 5451R → C in AAA35303 (PubMed:8443413).Curated
Sequence conflicti777 – 7848KLEFEKVY → NWSFST in CAA41968 (PubMed:1960723).Curated
Sequence conflicti866 – 8661L → H in CAA41968 (PubMed:1960723).Curated

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.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliP30316.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi276786. 33 interactions.
IntActiP30316. 1 interaction.
MINTiMINT-4688192.

Proteomic databases

MaxQBiP30316.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:SPBC336.04.
PomBaseiSPBC336.04.

Phylogenomic databases

HOGENOMiHOG000036616.
InParanoidiP30316.
KOiK02327.
OMAiEQASLCP.
OrthoDBiEOG092C0BQT.
PhylomeDBiP30316.

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-69109. Leading Strand Synthesis.
R-SPO-69166. Removal of the Flap Intermediate.
R-SPO-69183. Processive synthesis on the lagging strand.

Miscellaneous databases

PROiP30316.

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 nameiDPOD_SCHPO
AccessioniPrimary (citable) accession number: P30316
Secondary accession number(s): Q10016, Q9USU0, Q9UU61
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: January 11, 2001
Last modified: September 7, 2016
This is version 156 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal 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. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  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.