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P15436 (DPOD_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 148. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA polymerase delta catalytic subunit

EC=2.7.7.7
Alternative name(s):
DNA polymerase III
Gene names
Name:POL3
Synonyms:CDC2, TEX1
Ordered Locus Names:YDL102W
ORF Names:D2366
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length1097 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.6

Catalytic activity

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Cofactor

Binds 1 4Fe-4S cluster. Ref.12

Subunit structure

DNA polymerase delta is a heterotrimer of POL3, POL32 and HYS2. Interacts with PCNA. Ref.12

Subcellular location

Nucleus Ref.8.

Domain

The CysA-type zinc finger is required for PCNA-binding (Ref.12).

The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes (Ref.12).

Miscellaneous

In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis.

Sequence similarities

Belongs to the DNA polymerase type-B family.

Contains 1 CysA-type zinc finger.

Ontologies

Keywords
   Biological processDNA replication
   Cellular componentNucleus
   DomainZinc-finger
   Ligand4Fe-4S
DNA-binding
Iron
Iron-sulfur
Metal-binding
Zinc
   Molecular functionDNA-directed DNA polymerase
Exonuclease
Hydrolase
Nuclease
Nucleotidyltransferase
Transferase
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA catabolic process, exonucleolytic

Inferred from mutant phenotype Ref.6. Source: GOC

DNA replication

Inferred from mutant phenotype PubMed 1678279. Source: SGD

DNA replication, removal of RNA primer

Inferred from direct assay PubMed 16837458. Source: SGD

RNA-dependent DNA replication

Inferred from direct assay PubMed 17429354. Source: SGD

maintenance of fidelity involved in DNA-dependent DNA replication

Inferred from genetic interaction PubMed 15601866. Source: SGD

   Cellular_componentcytosol

Traceable author statement. Source: Reactome

delta DNA polymerase complex

Traceable author statement PubMed 9745046. Source: SGD

replication fork

Inferred from direct assay PubMed 15773893. Source: SGD

   Molecular_function3'-5'-exodeoxyribonuclease activity

Inferred from mutant phenotype Ref.6. Source: SGD

4 iron, 4 sulfur cluster binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA-directed DNA polymerase activity

Inferred from direct assay PubMed 1678279PubMed 18635534. Source: SGD

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

nucleotide binding

Inferred from electronic annotation. Source: InterPro

protein binding

Inferred from physical interaction PubMed 15173383PubMed 16429126. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

POL31P469573EBI-6134,EBI-6080

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 10971097DNA polymerase delta catalytic subunit
PRO_0000046454

Regions

Zinc finger1009 – 102719CysA-type
Motif1056 – 107419CysB motif

Sites

Metal binding10091Zinc
Metal binding10121Zinc
Metal binding10241Zinc
Metal binding10271Zinc
Metal binding10561Iron-sulfur (4Fe-4S)
Metal binding10591Iron-sulfur (4Fe-4S)
Metal binding10691Iron-sulfur (4Fe-4S)
Metal binding10741Iron-sulfur (4Fe-4S)

Amino acid modifications

Modified residue301Phosphoserine Ref.9 Ref.10 Ref.11
Modified residue371Phosphoserine Ref.11

Experimental info

Mutagenesis10091C → A: Impairs iron-sulfur-binding. Ref.12
Mutagenesis10121C → A: Impairs iron-sulfur-binding. Ref.12
Mutagenesis10241C → A: Impairs iron-sulfur-binding. Ref.12
Mutagenesis10271C → A: Impairs iron-sulfur-binding. Ref.12
Mutagenesis10561C → A: Abolishes iron-sulfur-binding. Ref.12
Mutagenesis10591C → A: Abolishes iron-sulfur-binding.
Mutagenesis10691C → A: Abolishes iron-sulfur-binding. Ref.12
Mutagenesis10741C → A: Abolishes iron-sulfur-binding. Ref.12
Mutagenesis10741C → S in pol3-13; synthetically lethal with mutations of NBP35, DRE2 and TAH18. Ref.12
Sequence conflict78 – 792EL → DV in CAA33504. Ref.1
Sequence conflict78 – 792EL → DV in CAA64911. Ref.3
Sequence conflict78 – 792EL → DV in CAA98669. Ref.4
Sequence conflict1891H → R in CAA33504. Ref.1
Sequence conflict2041G → D in CAA33504. Ref.1
Sequence conflict347 – 36317SIAGA…VFTLN → YLALRNHSFVMCYSD in CAA33504. Ref.1
Sequence conflict647 – 6493TPN → HY in CAA33504. Ref.1
Sequence conflict8701V → D in CAA33504. Ref.1
Sequence conflict9741Missing in CAA33504. Ref.1

Secondary structure

........................................................................................................................................... 1097
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P15436 [UniParc].

Last modified July 27, 2011. Version 4.
Checksum: 16E4245C5DCC66DB

FASTA1,097124,619
        10         20         30         40         50         60 
MSEKRSLPMV DVKIDDEDTP QLEKKIKRQS IDHGVGSEPV STIEIIPSDS FRKYNSQGFK 

        70         80         90        100        110        120 
AKDTDLMGTQ LESTFEQELS QMEHDMADQE EHDLSSFERK KLPTDFDPSL YDISFQQIDA 

       130        140        150        160        170        180 
EQSVLNGIKD ENTSTVVRFF GVTSEGHSVL CNVTGFKNYL YVPAPNSSDA NDQEQINKFV 

       190        200        210        220        230        240 
HYLNETFDHA IDSIEVVSKQ SIWGYSGDTK LPFWKIYVTY PHMVNKLRTA FERGHLSFNS 

       250        260        270        280        290        300 
WFSNGTTTYD NIAYTLRLMV DCGIVGMSWI TLPKGKYSMI EPNNRVSSCQ LEVSINYRNL 

       310        320        330        340        350        360 
IAHPAEGDWS HTAPLRIMSF DIECAGRIGV FPEPEYDPVI QIANVVSIAG AKKPFIRNVF 

       370        380        390        400        410        420 
TLNTCSPITG SMIFSHATEE EMLSNWRNFI IKVDPDVIIG YNTTNFDIPY LLNRAKALKV 

       430        440        450        460        470        480 
NDFPYFGRLK TVKQEIKESV FSSKAYGTRE TKNVNIDGRL QLDLLQFIQR EYKLRSYTLN 

       490        500        510        520        530        540 
AVSAHFLGEQ KEDVHYSIIS DLQNGDSETR RRLAVYCLKD AYLPLRLMEK LMALVNYTEM 

       550        560        570        580        590        600 
ARVTGVPFSY LLARGQQIKV VSQLFRKCLE IDTVIPNMQS QASDDQYEGA TVIEPIRGYY 

       610        620        630        640        650        660 
DVPIATLDFN SLYPSIMMAH NLCYTTLCNK ATVERLNLKI DEDYVITPNG DYFVTTKRRR 

       670        680        690        700        710        720 
GILPIILDEL ISARKRAKKD LRDEKDPFKR DVLNGRQLAL KISANSVYGF TGATVGKLPC 

       730        740        750        760        770        780 
LAISSSVTAY GRTMILKTKT AVQEKYCIKN GYKHDAVVVY GDTDSVMVKF GTTDLKEAMD 

       790        800        810        820        830        840 
LGTEAAKYVS TLFKHPINLE FEKAYFPYLL INKKRYAGLF WTNPDKFDKL DQKGLASVRR 

       850        860        870        880        890        900 
DSCSLVSIVM NKVLKKILIE RNVDGALAFV RETINDILHN RVDISKLIIS KTLAPNYTNP 

       910        920        930        940        950        960 
QPHAVLAERM KRREGVGPNV GDRVDYVIIG GNDKLYNRAE DPLFVLENNI QVDSRYYLTN 

       970        980        990       1000       1010       1020 
QLQNPIISIV APIIGDKQAN GMFVVKSIKI NTGSQKGGLM SFIKKVEACK SCKGPLRKGE 

      1030       1040       1050       1060       1070       1080 
GPLCSNCLAR SGELYIKALY DVRDLEEKYS RLWTQCQRCA GNLHSEVLCS NKNCDIFYMR 

      1090 
VKVKKELQEK VEQLSKW 

« Hide

References

« Hide 'large scale' references
[1]"Structure and function of the Saccharomyces cerevisiae CDC2 gene encoding the large subunit of DNA polymerase III."
Boulet A., Simon M., Faye G., Bauer G.A., Burgers M.J.
EMBO J. 8:1849-1854(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: YAB2.
[2]"Nucleotide sequence of the POL3 gene encoding DNA polymerase III (delta) of Saccharomyces cerevisiae."
Morrison A., Sugino A.
Nucleic Acids Res. 20:375-375(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SEQUENCE REVISION.
[3]"The sequence of a 20.3 kb DNA fragment from the left arm of Saccharomyces cerevisiae chromosome IV contains the KIN28, MSS2, PHO2, POL3 and DUN1 genes, and six new open reading frames."
Saiz J.E., Buitrago M.J., Garcia R., Revuelta J.L., del Rey F.
Yeast 12:1077-1084(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 96604 / S288c / FY1679.
[4]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. expand/collapse author list , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 78-79.
Strain: ATCC 204508 / S288c.
[6]"The 3' to 5' exonuclease activity located in the DNA polymerase delta subunit of Saccharomyces cerevisiae is required for accurate replication."
Simon M., Giot L., Faye G.
EMBO J. 10:2165-2170(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS AN EXONUCLEASE.
[7]"Structure of DNA polymerase delta from Saccharomyces cerevisiae."
Johansson E., Majka J., Burgers P.M.
J. Biol. Chem. 276:43824-43828(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: COMPOSITION OF THE DNA POLYMERASE DELTA COMPLEX.
[8]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[9]"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-30, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Strain: ADR376.
[10]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-30, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-30 AND SER-37, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"Eukaryotic DNA polymerases require an iron-sulfur cluster for the formation of active complexes."
Netz D.J., Stith C.M., Stumpfig M., Kopf G., Vogel D., Genau H.M., Stodola J.L., Lill R., Burgers P.M., Pierik A.J.
Nat. Chem. Biol. 8:125-132(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: COFACTOR, IRON-SULFUR-BINDING, ZINC-BINDING, INTERACTION WITH PCNA, MUTAGENESIS OF CYS-1009; CYS-1012; CYS-1024; CYS-1027; CYS-1056; CYS-1069; CYS-1069 AND CYS-1074.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRRNBYL3. S67644.
RefSeqNP_010181.2. NM_001180161.2.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3IAYX-ray2.00A67-985[»]
ProteinModelPortalP15436.
SMRP15436. Positions 95-985.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31960. 172 interactions.
DIPDIP-2524N.
IntActP15436. 4 interactions.
MINTMINT-2781941.
STRING4932.YDL102W.

Proteomic databases

MaxQBP15436.
PaxDbP15436.
PeptideAtlasP15436.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYDL102W; YDL102W; YDL102W.
GeneID851456.
KEGGsce:YDL102W.

Organism-specific databases

CYGDYDL102w.
SGDS000002260. POL3.

Phylogenomic databases

eggNOGCOG0417.
GeneTreeENSGT00560000077365.
HOGENOMHOG000036616.
KOK02327.
OMAQLFRKAN.
OrthoDBEOG7KSXJ9.

Enzyme and pathway databases

BioCycYEAST:G3O-29505-MONOMER.
ReactomeREACT_160098. Cytosolic iron-sulfur cluster assembly (yeast).
REACT_191296. Metabolism.

Gene expression databases

GenevestigatorP15436.

Family and domain databases

Gene3D3.30.420.10. 1 hit.
3.90.1600.10. 2 hits.
InterProIPR006172. 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.
IPR004578. DNA-dir_DNA_pol_B_pol2.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_dom.
IPR025687. Znf-C4pol.
[Graphical view]
PfamPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
PF14260. zf-C4pol. 1 hit.
[Graphical view]
PRINTSPR00106. DNAPOLB.
SMARTSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMSSF53098. SSF53098. 1 hit.
TIGRFAMsTIGR00592. pol2. 1 hit.
PROSITEPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio968726.
PROP15436.

Entry information

Entry nameDPOD_YEAST
AccessionPrimary (citable) accession number: P15436
Secondary accession number(s): D6VRP8
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: July 27, 2011
Last modified: June 11, 2014
This is version 148 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IV

Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references