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Q15054 (DPOD3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 123. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA polymerase delta subunit 3
Alternative name(s):
DNA polymerase delta subunit p66
Gene names
Name:POLD3
Synonyms:KIAA0039
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length466 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Required for optimal DNA polymerase delta activity. Ref.7 Ref.8 Ref.10

Subunit structure

Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. Interacts with POLD2. Interacts with PCNA. Ref.10

Subcellular location

Nucleus.

Sequence caution

The sequence BAA05039.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Biological processDNA replication
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   Molecular functionDNA-directed DNA polymerase
Nucleotidyltransferase
Transferase
   PTMAcetylation
Phosphoprotein
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processDNA repair

Traceable author statement. Source: Reactome

DNA strand elongation involved in DNA replication

Traceable author statement. Source: Reactome

DNA synthesis involved in DNA repair

Non-traceable author statement PubMed 7910606. Source: UniProtKB

base-excision repair

Traceable author statement. Source: Reactome

mismatch repair

Non-traceable author statement PubMed 9099749. Source: UniProtKB

mitotic cell cycle

Traceable author statement. Source: Reactome

nucleotide-excision repair

Traceable author statement. Source: Reactome

nucleotide-excision repair, DNA gap filling

Inferred from mutant phenotype PubMed 20227374. Source: UniProtKB

telomere maintenance

Traceable author statement. Source: Reactome

telomere maintenance via recombination

Traceable author statement. Source: Reactome

telomere maintenance via semi-conservative replication

Traceable author statement. Source: Reactome

transcription-coupled nucleotide-excision repair

Traceable author statement. Source: Reactome

   Cellular_componentdelta DNA polymerase complex

Non-traceable author statement Ref.7. Source: UniProtKB

mitochondrion

Inferred from direct assay. Source: HPA

nucleoplasm

Traceable author statement. Source: Reactome

nucleus

Inferred from direct assay. Source: HPA

   Molecular_functionDNA-directed DNA polymerase activity

Non-traceable author statement Ref.7. Source: UniProtKB

protein binding

Inferred from physical interaction PubMed 16000169Ref.10. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

PCNAP120044EBI-864956,EBI-358311
POLD2P490055EBI-864956,EBI-372354

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q15054-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q15054-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-39: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q15054-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-106: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.6
Chain2 – 466465DNA polymerase delta subunit 3
PRO_0000186047

Amino acid modifications

Modified residue21N-acetylalanine Ref.6 Ref.18
Modified residue3071Phosphoserine Ref.9 Ref.11 Ref.12 Ref.14 Ref.15 Ref.17
Modified residue4071Phosphoserine Ref.12
Modified residue4091Phosphoserine Ref.12
Modified residue4111Phosphothreonine Ref.12
Modified residue4131Phosphoserine Ref.12
Modified residue4581Phosphoserine Ref.12

Natural variations

Alternative sequence1 – 106106Missing in isoform 3.
VSP_054149
Alternative sequence1 – 3939Missing in isoform 2.
VSP_054150
Natural variant1941G → V Found in a renal cell carcinoma sample; somatic mutation. Ref.19
VAR_064745
Natural variant1951M → L Found in a renal cell carcinoma sample; somatic mutation. Ref.19
VAR_064746

Secondary structure

........................ 466
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified September 26, 2001. Version 2.
Checksum: E9625E0188725F45

FASTA46651,400
        10         20         30         40         50         60 
MADQLYLENI DEFVTDQNKI VTYKWLSYTL GVHVNQAKQM LYDYVERKRK ENSGAQLHVT 

        70         80         90        100        110        120 
YLVSGSLIQN GHSCHKVAVV REDKLEAVKS KLAVTASIHV YSIQKAMLKD SGPLFNTDYD 

       130        140        150        160        170        180 
ILKSNLQNCS KFSAIQCAAA VPRAPAESSS SSKKFEQSHL HMSSETQANN ELTTNGHGPP 

       190        200        210        220        230        240 
ASKQVSQQPK GIMGMFASKA AAKTQETNKE TKTEAKEVTN ASAAGNKAPG KGNMMSNFFG 

       250        260        270        280        290        300 
KAAMNKFKVN LDSEQAVKEE KIVEQPTVSV TEPKLATPAG LKKSSKKAEP VKVLQKEKKR 

       310        320        330        340        350        360 
GKRVALSDDE TKETENMRKK RRRIKLPESD SSEDEVFPDS PGAYEAESPS PPPPPSPPLE 

       370        380        390        400        410        420 
PVPKTEPEPP SVKSSSGENK RKRKRVLKSK TYLDGEGCIV TEKVYESESC TDSEEELNMK 

       430        440        450        460 
TSSVHRPPAM TVKKEPREER KGPKKGTAAL GKANRQVSIT GFFQRK 

« Hide

Isoform 2 [UniParc].

Checksum: 29070FF3F00F0BCB
Show »

FASTA42746,801
Isoform 3 [UniParc].

Checksum: 70ACBAD78175C9BC
Show »

FASTA36039,320

References

« Hide 'large scale' references
[1]"Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1."
Nomura N., Miyajima N., Sazuka T., Tanaka A., Kawarabayasi Y., Sato S., Nagase T., Seki N., Ishikawa K., Tabata S.
DNA Res. 1:27-35(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Bone marrow.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Placenta.
[3]"Human chromosome 11 DNA sequence and analysis including novel gene identification."
Taylor T.D., Noguchi H., Totoki Y., Toyoda A., Kuroki Y., Dewar K., Lloyd C., Itoh T., Takeda T., Kim D.-W., She X., Barlow K.F., Bloom T., Bruford E., Chang J.L., Cuomo C.A., Eichler E., FitzGerald M.G. expand/collapse author list , Jaffe D.B., LaButti K., Nicol R., Park H.-S., Seaman C., Sougnez C., Yang X., Zimmer A.R., Zody M.C., Birren B.W., Nusbaum C., Fujiyama A., Hattori M., Rogers J., Lander E.S., Sakaki Y.
Nature 440:497-500(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3).
[6]Bienvenut W.V., Waridel P., Quadroni M.
Submitted (MAR-2009) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 2-19 AND 110-123, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY.
Tissue: Embryonic kidney.
[7]"Isolation and identification of the third subunit of mammalian DNA polymerase delta by PCNA-affinity chromatography of mouse FM3A cell extracts."
Hughes P., Tratner I., Ducoux M., Piard K., Baldacci G.
Nucleic Acids Res. 27:2108-2114(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"Evidence that DNA polymerase delta isolated by immunoaffinity chromatography exhibits high-molecular weight characteristics and is associated with the KIAA0039 protein and RPA."
Mo J.-Y., Liu L., Leon A., Mazloum N., Lee M.Y.W.T.
Biochemistry 39:7245-7254(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[9]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-307, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"Functional roles of p12, the fourth subunit of human DNA polymerase delta."
Li H., Xie B., Zhou Y., Rahmeh A., Trusa S., Zhang S., Gao Y., Lee E.Y., Lee M.Y.
J. Biol. Chem. 281:14748-14755(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH PCNA.
[11]"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle."
Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M.
Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-307, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[12]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-307; SER-407; SER-409; THR-411; SER-413 AND SER-458, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[13]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"Large-scale proteomics analysis of the human kinome."
Oppermann F.S., Gnad F., Olsen J.V., Hornberger R., Greff Z., Keri G., Mann M., Daub H.
Mol. Cell. Proteomics 8:1751-1764(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-307, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-307, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[16]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[17]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-307, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[18]"Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[19]"Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma."
Varela I., Tarpey P., Raine K., Huang D., Ong C.K., Stephens P., Davies H., Jones D., Lin M.L., Teague J., Bignell G., Butler A., Cho J., Dalgliesh G.L., Galappaththige D., Greenman C., Hardy C., Jia M. expand/collapse author list , Latimer C., Lau K.W., Marshall J., McLaren S., Menzies A., Mudie L., Stebbings L., Largaespada D.A., Wessels L.F.A., Richard S., Kahnoski R.J., Anema J., Tuveson D.A., Perez-Mancera P.A., Mustonen V., Fischer A., Adams D.J., Rust A., Chan-On W., Subimerb C., Dykema K., Furge K., Campbell P.J., Teh B.T., Stratton M.R., Futreal P.A.
Nature 469:539-542(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS VAL-194 AND LEU-195.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D26018 mRNA. Translation: BAA05039.1. Different initiation.
AK316301 mRNA. Translation: BAH14672.1.
AP001104 Genomic DNA. No translation available.
AP001324 Genomic DNA. No translation available.
AP001372 Genomic DNA. No translation available.
CH471076 Genomic DNA. Translation: EAW74942.1.
BC108908 mRNA. Translation: AAI08909.1.
BC108909 mRNA. Translation: AAI08910.1.
CCDSCCDS8233.1.
RefSeqNP_006582.1. NM_006591.2. [Q15054-1]
UniGeneHs.82502.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1U76X-ray2.60B/D/F452-466[»]
3E0JX-ray3.00B/D/F/H1-144[»]
ProteinModelPortalQ15054.
SMRQ15054. Positions 2-144.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid115940. 22 interactions.
DIPDIP-35772N.
IntActQ15054. 6 interactions.
MINTMINT-2789689.
STRING9606.ENSP00000263681.

PTM databases

PhosphoSiteQ15054.

Polymorphism databases

DMDM17375506.

Proteomic databases

MaxQBQ15054.
PaxDbQ15054.
PeptideAtlasQ15054.
PRIDEQ15054.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000263681; ENSP00000263681; ENSG00000077514.
ENST00000527458; ENSP00000432951; ENSG00000077514.
ENST00000532497; ENSP00000436018; ENSG00000077514.
GeneID10714.
KEGGhsa:10714.
UCSCuc001ovf.2. human. [Q15054-1]

Organism-specific databases

CTD10714.
GeneCardsGC11P074207.
HGNCHGNC:20932. POLD3.
HPAHPA039627.
MIM611415. gene.
neXtProtNX_Q15054.
PharmGKBPA134868595.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG83700.
HOGENOMHOG000008055.
HOVERGENHBG051397.
InParanoidQ15054.
KOK03504.
OMAVMSNFFG.
PhylomeDBQ15054.
TreeFamTF103006.

Enzyme and pathway databases

ReactomeREACT_115566. Cell Cycle.
REACT_216. DNA Repair.
REACT_383. DNA Replication.

Gene expression databases

ArrayExpressQ15054.
BgeeQ15054.
GenevestigatorQ15054.

Family and domain databases

InterProIPR019038. DNA_polymerase_subunit_Cdc27.
[Graphical view]
PfamPF09507. CDC27. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ15054.
GeneWikiPOLD3.
GenomeRNAi10714.
NextBio40675.
PROQ15054.
SOURCESearch...

Entry information

Entry nameDPOD3_HUMAN
AccessionPrimary (citable) accession number: Q15054
Secondary accession number(s): B7ZAI6, Q32MZ9, Q32N00
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: September 26, 2001
Last modified: July 9, 2014
This is version 123 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 11

Human chromosome 11: entries, gene names and cross-references to MIM