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: Annotation score: 5 out of 5-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

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

  • base-excision repair, gap-filling Source: GO_Central
  • DNA-dependent DNA replication maintenance of fidelity Source: SGD
  • DNA replication Source: SGD
  • DNA replication, removal of RNA primer Source: SGD
  • DNA replication proofreading Source: GO_Central
  • nucleotide-excision repair, DNA gap filling Source: GO_Central
  • RNA-dependent DNA biosynthetic process Source: SGD
  • small molecule metabolic process Source: Reactome
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

BioCyciYEAST:G3O-29505-MONOMER.
ReactomeiR-SCE-2564818. Cytosolic iron-sulfur cluster assembly (yeast).
R-SCE-2564830. Cytosolic iron-sulfur cluster assembly.
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

EuPathDBiFungiDB:YDL102W.
SGDiS000002260. POL3.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • delta DNA polymerase complex Source: SGD
  • replication fork Source: SGD
Complete GO annotation...

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.
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
POL31P469573EBI-6134,EBI-6080

Protein-protein interaction databases

BioGridi31960. 196 interactors.
DIPiDIP-2524N.
IntActiP15436. 4 interactors.
MINTiMINT-2781941.

Structurei

Secondary structure

11097
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni108 – 110Combined sources3
Beta strandi113 – 124Combined sources12
Beta strandi126 – 128Combined sources3
Beta strandi135 – 143Combined sources9
Beta strandi148 – 155Combined sources8
Beta strandi159 – 163Combined sources5
Helixi168 – 171Combined sources4
Helixi173 – 184Combined sources12
Turni185 – 189Combined sources5
Beta strandi191 – 203Combined sources13
Beta strandi211 – 220Combined sources10
Helixi223 – 233Combined sources11
Helixi238 – 240Combined sources3
Helixi254 – 262Combined sources9
Beta strandi269 – 272Combined sources4
Helixi282 – 284Combined sources3
Beta strandi290 – 296Combined sources7
Turni297 – 299Combined sources3
Beta strandi301 – 303Combined sources3
Helixi307 – 309Combined sources3
Beta strandi316 – 324Combined sources9
Turni334 – 336Combined sources3
Beta strandi339 – 348Combined sources10
Beta strandi355 – 363Combined sources9
Beta strandi371 – 378Combined sources8
Helixi379 – 393Combined sources15
Beta strandi396 – 402Combined sources7
Turni403 – 406Combined sources4
Helixi407 – 417Combined sources11
Beta strandi427 – 429Combined sources3
Beta strandi439 – 443Combined sources5
Turni444 – 446Combined sources3
Beta strandi447 – 451Combined sources5
Beta strandi460 – 463Combined sources4
Helixi464 – 471Combined sources8
Helixi479 – 487Combined sources9
Helixi499 – 503Combined sources5
Helixi507 – 530Combined sources24
Helixi533 – 544Combined sources12
Helixi550 – 553Combined sources4
Helixi556 – 570Combined sources15
Beta strandi598 – 600Combined sources3
Beta strandi604 – 609Combined sources6
Helixi612 – 619Combined sources8
Helixi624 – 626Combined sources3
Helixi630 – 635Combined sources6
Turni641 – 643Combined sources3
Beta strandi644 – 646Combined sources3
Beta strandi652 – 654Combined sources3
Turni656 – 658Combined sources3
Helixi662 – 682Combined sources21
Helixi687 – 711Combined sources25
Beta strandi714 – 717Combined sources4
Helixi721 – 745Combined sources25
Helixi748 – 750Combined sources3
Beta strandi757 – 760Combined sources4
Beta strandi762 – 769Combined sources8
Helixi775 – 790Combined sources16
Beta strandi799 – 812Combined sources14
Beta strandi815 – 826Combined sources12
Beta strandi829 – 835Combined sources7
Helixi836 – 838Combined sources3
Helixi844 – 858Combined sources15
Helixi863 – 878Combined sources16
Helixi884 – 887Combined sources4
Beta strandi889 – 892Combined sources4
Helixi902 – 914Combined sources13
Beta strandi922 – 929Combined sources8
Beta strandi931 – 933Combined sources3
Helixi935 – 937Combined sources3
Helixi942 – 947Combined sources6
Helixi954 – 960Combined sources7
Helixi963 – 974Combined sources12
Helixi976 – 982Combined sources7

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...

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
Contains 1 CysA-type zinc finger.Curated

Zinc finger

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

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00560000077365.
HOGENOMiHOG000036616.
InParanoidiP15436.
KOiK02327.
OMAiEGHSVLC.
OrthoDBiEOG092C0BQT.

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.

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.

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. 196 interactors.
DIPiDIP-2524N.
IntActiP15436. 4 interactors.
MINTiMINT-2781941.

PTM databases

iPTMnetiP15436.

Proteomic databases

MaxQBiP15436.
PRIDEiP15436.
TopDownProteomicsiP15436.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL102W; YDL102W; YDL102W.
GeneIDi851456.
KEGGisce:YDL102W.

Organism-specific databases

EuPathDBiFungiDB:YDL102W.
SGDiS000002260. POL3.

Phylogenomic databases

GeneTreeiENSGT00560000077365.
HOGENOMiHOG000036616.
InParanoidiP15436.
KOiK02327.
OMAiEGHSVLC.
OrthoDBiEOG092C0BQT.

Enzyme and pathway databases

BioCyciYEAST:G3O-29505-MONOMER.
ReactomeiR-SCE-2564818. Cytosolic iron-sulfur cluster assembly (yeast).
R-SCE-2564830. Cytosolic iron-sulfur cluster assembly.
R-SCE-69166. Removal of the Flap Intermediate.
R-SCE-69183. Processive synthesis on the lagging strand.

Miscellaneous databases

PROiP15436.

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_YEAST
AccessioniPrimary (citable) accession number: P15436
Secondary accession number(s): D6VRP8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: July 27, 2011
Last modified: November 30, 2016
This is version 173 of the entry and version 4 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  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

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.