Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

DNA polymerase delta catalytic subunit

Gene

POL3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. POL3 contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity.1 Publication

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] cluster1 PublicationNote: Binds 1 [4Fe-4S] cluster.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1009Zinc1
Metal bindingi1012Zinc1
Metal bindingi1024Zinc1
Metal bindingi1027Zinc1
Metal bindingi1056Iron-sulfur (4Fe-4S)1
Metal bindingi1059Iron-sulfur (4Fe-4S)1
Metal bindingi1069Iron-sulfur (4Fe-4S)1
Metal bindingi1074Iron-sulfur (4Fe-4S)1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1009 – 1027CysA-typeAdd BLAST19

GO - Molecular functioni

  • 3'-5'-exodeoxyribonuclease activity Source: SGD
  • 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  • DNA binding Source: UniProtKB-KW
  • DNA-directed DNA polymerase activity Source: SGD
  • 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

BioCyciYEAST:G3O-29505-MONOMER
ReactomeiR-SCE-2564818 Cytosolic iron-sulfur cluster assembly (yeast)
R-SCE-69166 Removal of the Flap Intermediate
R-SCE-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:CDC2, TEX1
Ordered Locus Names:YDL102W
ORF Names:D2366
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

SGDiS000002260 POL3

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1009C → A: Impairs iron-sulfur-binding. 1 Publication1
Mutagenesisi1012C → A: Impairs iron-sulfur-binding. 1 Publication1
Mutagenesisi1024C → A: Impairs iron-sulfur-binding. 1 Publication1
Mutagenesisi1027C → A: Impairs iron-sulfur-binding. 1 Publication1
Mutagenesisi1056C → A: Abolishes iron-sulfur-binding. 1 Publication1
Mutagenesisi1059C → A: Abolishes iron-sulfur-binding. 1
Mutagenesisi1069C → A: Abolishes iron-sulfur-binding. 1 Publication1
Mutagenesisi1074C → A: Abolishes iron-sulfur-binding. 1 Publication1
Mutagenesisi1074C → S in pol3-13; synthetically lethal with mutations of NBP35, DRE2 and TAH18. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000464541 – 1097DNA polymerase delta catalytic subunitAdd BLAST1097

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei30PhosphoserineCombined sources1
Modified residuei37PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP15436
PaxDbiP15436
PRIDEiP15436
TopDownProteomicsiP15436

PTM databases

iPTMnetiP15436

Interactioni

Subunit structurei

DNA polymerase delta is a heterotrimer of POL3, POL32 and HYS2. Interacts with PCNA.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
POL31P469575EBI-6134,EBI-6080

Protein-protein interaction databases

BioGridi31960, 669 interactors
ComplexPortaliCPX-2101 DNA polymerase delta complex
DIPiDIP-2524N
IntActiP15436, 5 interactors
MINTiP15436
STRINGi4932.YDL102W

Structurei

Secondary structure

11097
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP15436
SMRiP15436
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1056 – 1074CysB motifAdd BLAST19

Domaini

The CysA-type zinc finger is required for PCNA-binding.1 Publication
The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes.1 Publication

Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1009 – 1027CysA-typeAdd BLAST19

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00560000077365
HOGENOMiHOG000036616
InParanoidiP15436
KOiK02327
OMAiCLVNYTE
OrthoDBiEOG092C0BQT

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_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.

P15436-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSEKRSLPMV DVKIDDEDTP QLEKKIKRQS IDHGVGSEPV STIEIIPSDS
60 70 80 90 100
FRKYNSQGFK AKDTDLMGTQ LESTFEQELS QMEHDMADQE EHDLSSFERK
110 120 130 140 150
KLPTDFDPSL YDISFQQIDA EQSVLNGIKD ENTSTVVRFF GVTSEGHSVL
160 170 180 190 200
CNVTGFKNYL YVPAPNSSDA NDQEQINKFV HYLNETFDHA IDSIEVVSKQ
210 220 230 240 250
SIWGYSGDTK LPFWKIYVTY PHMVNKLRTA FERGHLSFNS WFSNGTTTYD
260 270 280 290 300
NIAYTLRLMV DCGIVGMSWI TLPKGKYSMI EPNNRVSSCQ LEVSINYRNL
310 320 330 340 350
IAHPAEGDWS HTAPLRIMSF DIECAGRIGV FPEPEYDPVI QIANVVSIAG
360 370 380 390 400
AKKPFIRNVF TLNTCSPITG SMIFSHATEE EMLSNWRNFI IKVDPDVIIG
410 420 430 440 450
YNTTNFDIPY LLNRAKALKV NDFPYFGRLK TVKQEIKESV FSSKAYGTRE
460 470 480 490 500
TKNVNIDGRL QLDLLQFIQR EYKLRSYTLN AVSAHFLGEQ KEDVHYSIIS
510 520 530 540 550
DLQNGDSETR RRLAVYCLKD AYLPLRLMEK LMALVNYTEM ARVTGVPFSY
560 570 580 590 600
LLARGQQIKV VSQLFRKCLE IDTVIPNMQS QASDDQYEGA TVIEPIRGYY
610 620 630 640 650
DVPIATLDFN SLYPSIMMAH NLCYTTLCNK ATVERLNLKI DEDYVITPNG
660 670 680 690 700
DYFVTTKRRR GILPIILDEL ISARKRAKKD LRDEKDPFKR DVLNGRQLAL
710 720 730 740 750
KISANSVYGF TGATVGKLPC LAISSSVTAY GRTMILKTKT AVQEKYCIKN
760 770 780 790 800
GYKHDAVVVY GDTDSVMVKF GTTDLKEAMD LGTEAAKYVS TLFKHPINLE
810 820 830 840 850
FEKAYFPYLL INKKRYAGLF WTNPDKFDKL DQKGLASVRR DSCSLVSIVM
860 870 880 890 900
NKVLKKILIE RNVDGALAFV RETINDILHN RVDISKLIIS KTLAPNYTNP
910 920 930 940 950
QPHAVLAERM KRREGVGPNV GDRVDYVIIG GNDKLYNRAE DPLFVLENNI
960 970 980 990 1000
QVDSRYYLTN QLQNPIISIV APIIGDKQAN GMFVVKSIKI NTGSQKGGLM
1010 1020 1030 1040 1050
SFIKKVEACK SCKGPLRKGE GPLCSNCLAR SGELYIKALY DVRDLEEKYS
1060 1070 1080 1090
RLWTQCQRCA GNLHSEVLCS NKNCDIFYMR VKVKKELQEK VEQLSKW
Length:1,097
Mass (Da):124,619
Last modified:July 27, 2011 - v4
Checksum:i16E4245C5DCC66DB
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti78 – 79EL → DV in CAA33504 (PubMed:2670563).Curated2
Sequence conflicti78 – 79EL → DV in CAA64911 (PubMed:8896274).Curated2
Sequence conflicti78 – 79EL → DV in CAA98669 (PubMed:9169867).Curated2
Sequence conflicti189H → R in CAA33504 (PubMed:2670563).Curated1
Sequence conflicti204G → D in CAA33504 (PubMed:2670563).Curated1
Sequence conflicti347 – 363SIAGA…VFTLN → YLALRNHSFVMCYSD in CAA33504 (PubMed:2670563).CuratedAdd BLAST17
Sequence conflicti647 – 649TPN → HY in CAA33504 (PubMed:2670563).Curated3
Sequence conflicti870V → D in CAA33504 (PubMed:2670563).Curated1
Sequence conflicti974Missing in CAA33504 (PubMed:2670563).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15477 Genomic DNA Translation: CAA33504.1
X61920 Genomic DNA Translation: CAA43922.1
X95644 Genomic DNA Translation: CAA64911.1
Z74150 Genomic DNA Translation: CAA98669.1
BK006938 Genomic DNA Translation: DAA11758.2
PIRiS67644 RNBYL3
RefSeqiNP_010181.2, NM_001180161.2

Genome annotation databases

EnsemblFungiiYDL102W; YDL102W; YDL102W
GeneIDi851456
KEGGisce:YDL102W

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15477 Genomic DNA Translation: CAA33504.1
X61920 Genomic DNA Translation: CAA43922.1
X95644 Genomic DNA Translation: CAA64911.1
Z74150 Genomic DNA Translation: CAA98669.1
BK006938 Genomic DNA Translation: DAA11758.2
PIRiS67644 RNBYL3
RefSeqiNP_010181.2, NM_001180161.2

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3IAYX-ray2.00A67-985[»]
ProteinModelPortaliP15436
SMRiP15436
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31960, 669 interactors
ComplexPortaliCPX-2101 DNA polymerase delta complex
DIPiDIP-2524N
IntActiP15436, 5 interactors
MINTiP15436
STRINGi4932.YDL102W

PTM databases

iPTMnetiP15436

Proteomic databases

MaxQBiP15436
PaxDbiP15436
PRIDEiP15436
TopDownProteomicsiP15436

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL102W; YDL102W; YDL102W
GeneIDi851456
KEGGisce:YDL102W

Organism-specific databases

SGDiS000002260 POL3

Phylogenomic databases

GeneTreeiENSGT00560000077365
HOGENOMiHOG000036616
InParanoidiP15436
KOiK02327
OMAiCLVNYTE
OrthoDBiEOG092C0BQT

Enzyme and pathway databases

BioCyciYEAST:G3O-29505-MONOMER
ReactomeiR-SCE-2564818 Cytosolic iron-sulfur cluster assembly (yeast)
R-SCE-69166 Removal of the Flap Intermediate
R-SCE-69183 Processive synthesis on the lagging strand

Miscellaneous databases

PROiPR:P15436

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_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
ProtoNetiSearch...

Entry informationi

Entry nameiDPOD_YEAST
AccessioniPrimary (citable) accession number: P15436
Secondary accession number(s): D6VRP8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: July 27, 2011
Last modified: November 7, 2018
This is version 191 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again