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P52431

- DPOD1_MOUSE

UniProt

P52431 - DPOD1_MOUSE

Protein

DNA polymerase delta catalytic subunit

Gene

Pold1

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 122 (01 Oct 2014)
      Sequence version 2 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    Possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. Required with its accessory proteins (proliferating cell nuclear antigen (PCNA) and replication factor C (RFC) or activator 1) for leading strand synthesis. Also involved in completing Okazaki fragments initiated by the DNA polymerase alpha/primase complex.

    Catalytic activityi

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

    Cofactori

    Binds 1 4Fe-4S cluster.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi1010 – 10101ZincBy similarity
    Metal bindingi1013 – 10131ZincBy similarity
    Metal bindingi1024 – 10241ZincBy similarity
    Metal bindingi1027 – 10271ZincBy similarity
    Metal bindingi1056 – 10561Iron-sulfur (4Fe-4S)By similarity
    Metal bindingi1059 – 10591Iron-sulfur (4Fe-4S)By similarity
    Metal bindingi1069 – 10691Iron-sulfur (4Fe-4S)By similarity
    Metal bindingi1074 – 10741Iron-sulfur (4Fe-4S)By similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri1010 – 102718CysA-typeAdd
    BLAST

    GO - Molecular functioni

    1. 3'-5' exonuclease activity Source: MGI
    2. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
    3. chromatin binding Source: Ensembl
    4. DNA binding Source: UniProtKB-KW
    5. DNA-directed DNA polymerase activity Source: RefGenome
    6. metal ion binding Source: UniProtKB-KW
    7. nucleotide binding Source: InterPro

    GO - Biological processi

    1. base-excision repair, gap-filling Source: MGI
    2. DNA replication, removal of RNA primer Source: RefGenome
    3. DNA replication proofreading Source: MGI
    4. DNA synthesis involved in DNA repair Source: Ensembl
    5. fatty acid homeostasis Source: UniProtKB
    6. nucleic acid phosphodiester bond hydrolysis Source: GOC
    7. nucleotide-excision repair, DNA gap filling Source: RefGenome
    8. regulation of mitotic cell cycle Source: RefGenome

    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

    ReactomeiREACT_196637. Cytosolic iron-sulfur cluster assembly.
    REACT_209299. Repair synthesis of patch ~27-30 bases long by DNA polymerase.
    REACT_216529. Removal of the Flap Intermediate from the C-strand.
    REACT_219337. Removal of DNA patch containing abasic residue.
    REACT_219381. Repair synthesis for gap-filling by DNA polymerase in TC-NER.
    REACT_220175. Telomere C-strand (Lagging Strand) Synthesis.
    REACT_223154. Processive synthesis on the C-strand of the telomere.
    REACT_225604. Polymerase switching on the C-strand of the telomere.
    REACT_227394. Resolution of AP sites via the multiple-nucleotide patch replacement pathway.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA polymerase delta catalytic subunit (EC:2.7.7.7)
    Gene namesi
    Name:Pold1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 7

    Organism-specific databases

    MGIiMGI:97741. Pold1.

    Subcellular locationi

    GO - Cellular componenti

    1. delta DNA polymerase complex Source: RefGenome
    2. nucleotide-excision repair complex Source: Ensembl
    3. nucleus Source: RefGenome

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 11051105DNA polymerase delta catalytic subunitPRO_0000046444Add
    BLAST

    Proteomic databases

    MaxQBiP52431.
    PaxDbiP52431.
    PRIDEiP52431.

    PTM databases

    PhosphoSiteiP52431.

    Miscellaneous databases

    PMAP-CutDBP52431.

    Expressioni

    Gene expression databases

    BgeeiP52431.
    GenevestigatoriP52431.

    Interactioni

    Subunit structurei

    Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. The 125 kDa subunit contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity. Interacts with WRNIP1. Interacts with POLD4 and PCNA By similarity.By similarity

    Protein-protein interaction databases

    BioGridi202290. 3 interactions.
    DIPiDIP-45885N.
    IntActiP52431. 1 interaction.
    STRINGi10090.ENSMUSP00000039776.

    Structurei

    3D structure databases

    ProteinModelPortaliP52431.
    SMRiP52431. Positions 297-969.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi4 – 1916Nuclear localization signalSequence AnalysisAdd
    BLAST
    Motifi1056 – 107419CysB 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 fingeri1010 – 102718CysA-typeAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG0417.
    GeneTreeiENSGT00560000077365.
    HOGENOMiHOG000036616.
    HOVERGENiHBG051395.
    InParanoidiQ3TFX6.
    KOiK02327.
    OMAiQLFRKAN.
    OrthoDBiEOG7992PP.
    TreeFamiTF352785.

    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.

    P52431-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDCKRRQGPG PGVPPKRARG HLWDEDEPSP SQFEANLALL EEIEAENRLQ     50
    EAEEELQLPP EGTVGGQFST ADIDPRWRRP TLRALDPSTE PLIFQQLEID 100
    HYVGSAPPLP EGPLPSRNSV PILRAFGVTD EGFSVCCHIQ GFAPYFYTPA 150
    PPGFGAEHLS ELQQELNAAI SRDQRGGKEL SGPAVLAIEL CSRESMFGYH 200
    GHGPSPFLRI TLALPRLMAP ARRLLEQGVR VPGLGTPSFA PYEANVDFEI 250
    RFMVDADIVG CNWLELPAGK YVRRAEKKAT LCQLEVDVLW SDVISHPPEG 300
    QWQRIAPLRV LSFDIECAGR KGIFPEPERD PVIQICSLGL RWGEPEPFLR 350
    LALTLRPCAP ILGAKVQSYE REEDLLQAWA DFILAMDPDV ITGYNIQNFD 400
    LPYLISRAQA LKVDRFPFLG RVTGLRSNIR DSSFQSRQVG RRDSKVISMV 450
    GRVQMDMLQV LLREHKLRSY TLNAVSFHFL GEQKEDVQHS IITDLQNGNE 500
    QTRRRLAVYC LKDAFLPLRL LERLMVLVNN VEMARVTGVP LGYLLTRGQQ 550
    VKVVSQLLRQ AMRQGLLMPV VKTEGSEDYT GATVIEPLKG YYDVPIATLD 600
    FSSLYPSIMM AHNLCYTTLL RPGAAQKLGL KPDEFIKTPT GDEFVKSSVR 650
    KGLLPQILEN LLSARKRAKA ELAQETDPLR RQVLDGRQLA LKVSANSVYG 700
    FTGAQVGKLP CLEISQSVTG FGRQMIEKTK QLVESKYTVE NGYDANAKVV 750
    YGDTDSVMCR FGVSSVAEAM SLGREAANWV SSHFPSPIRL EFEKVYFPYL 800
    LISKKRYAGL LFSSRSDAHD KMDCKGLEAV RRDNCPLVAN LVTSSLRRIL 850
    VDRDPDGAVA HAKDVISDLL CNRIDISQLV ITKELTRAAA DYAGKQAHVE 900
    LAERMRKRDP GSAPSLGDRV PYVIIGAAKG VAAYMKSEDP LFVLEHSLPI 950
    DTQYYLEQQL AKPLLRIFEP ILGEGRAESV LLRGDHTRCK TVLTSKVGGL 1000
    LAFTKRRNCC IGCRSVIDHQ GAVCKFCQPR ESELYQKEVS HLNALEERFS 1050
    RLWTQCQRCQ GSLHEDVICT SRDCPIFYMR KKVRKDLEDQ ERLLQRFGPP 1100
    GPEAW 1105
    Length:1,105
    Mass (Da):123,790
    Last modified:July 27, 2011 - v2
    Checksum:i2AE377D42E3A6A86
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti112 – 1121G → R in CAA79895. (PubMed:8262377)Curated
    Sequence conflicti114 – 1141L → P in AAB99910. (PubMed:9434960)Curated
    Sequence conflicti576 – 5761S → G in CAA79895. (PubMed:8262377)Curated
    Sequence conflicti576 – 5761S → G in AAB99910. (PubMed:9434960)Curated
    Sequence conflicti793 – 7931E → K in AAB99910. (PubMed:9434960)Curated
    Sequence conflicti1000 – 10001L → F in AAB99910. (PubMed:9434960)Curated
    Sequence conflicti1035 – 10351Y → S in CAA79895. (PubMed:8262377)Curated
    Sequence conflicti1045 – 10528LEERFSRL → WKNGSLRF in AAB99910. (PubMed:9434960)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z21848 mRNA. Translation: CAA79895.1.
    AF024570 Genomic DNA. Translation: AAB99910.1.
    AK167569 mRNA. Translation: BAE39632.1.
    AK168967 mRNA. Translation: BAE40772.1.
    AK169040 mRNA. Translation: BAE40829.1.
    CCDSiCCDS21210.1.
    PIRiS40243.
    RefSeqiNP_035261.3. NM_011131.3.
    UniGeneiMm.16549.

    Genome annotation databases

    EnsembliENSMUST00000049343; ENSMUSP00000039776; ENSMUSG00000038644.
    GeneIDi18971.
    KEGGimmu:18971.
    UCSCiuc009gpx.2. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z21848 mRNA. Translation: CAA79895.1 .
    AF024570 Genomic DNA. Translation: AAB99910.1 .
    AK167569 mRNA. Translation: BAE39632.1 .
    AK168967 mRNA. Translation: BAE40772.1 .
    AK169040 mRNA. Translation: BAE40829.1 .
    CCDSi CCDS21210.1.
    PIRi S40243.
    RefSeqi NP_035261.3. NM_011131.3.
    UniGenei Mm.16549.

    3D structure databases

    ProteinModelPortali P52431.
    SMRi P52431. Positions 297-969.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 202290. 3 interactions.
    DIPi DIP-45885N.
    IntActi P52431. 1 interaction.
    STRINGi 10090.ENSMUSP00000039776.

    PTM databases

    PhosphoSitei P52431.

    Proteomic databases

    MaxQBi P52431.
    PaxDbi P52431.
    PRIDEi P52431.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000049343 ; ENSMUSP00000039776 ; ENSMUSG00000038644 .
    GeneIDi 18971.
    KEGGi mmu:18971.
    UCSCi uc009gpx.2. mouse.

    Organism-specific databases

    CTDi 5424.
    MGIi MGI:97741. Pold1.

    Phylogenomic databases

    eggNOGi COG0417.
    GeneTreei ENSGT00560000077365.
    HOGENOMi HOG000036616.
    HOVERGENi HBG051395.
    InParanoidi Q3TFX6.
    KOi K02327.
    OMAi QLFRKAN.
    OrthoDBi EOG7992PP.
    TreeFami TF352785.

    Enzyme and pathway databases

    Reactomei REACT_196637. Cytosolic iron-sulfur cluster assembly.
    REACT_209299. Repair synthesis of patch ~27-30 bases long by DNA polymerase.
    REACT_216529. Removal of the Flap Intermediate from the C-strand.
    REACT_219337. Removal of DNA patch containing abasic residue.
    REACT_219381. Repair synthesis for gap-filling by DNA polymerase in TC-NER.
    REACT_220175. Telomere C-strand (Lagging Strand) Synthesis.
    REACT_223154. Processive synthesis on the C-strand of the telomere.
    REACT_225604. Polymerase switching on the C-strand of the telomere.
    REACT_227394. Resolution of AP sites via the multiple-nucleotide patch replacement pathway.

    Miscellaneous databases

    ChiTaRSi POLD1. mouse.
    NextBioi 295320.
    PMAP-CutDB P52431.
    PROi P52431.
    SOURCEi Search...

    Gene expression databases

    Bgeei P52431.
    Genevestigatori P52431.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    3.90.1600.10. 2 hits.
    InterProi 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.
    IPR012337. RNaseH-like_dom.
    IPR025687. Znf-C4pol.
    [Graphical view ]
    Pfami PF00136. DNA_pol_B. 1 hit.
    PF03104. DNA_pol_B_exo1. 1 hit.
    PF14260. zf-C4pol. 1 hit.
    [Graphical view ]
    PRINTSi PR00106. DNAPOLB.
    SMARTi SM00486. POLBc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53098. SSF53098. 1 hit.
    PROSITEi PS00116. DNA_POLYMERASE_B. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning of a mouse cDNA encoding DNA polymerase delta: refinement of the homology boxes."
      Cullmann G., Hindges R., Berchtold M.W., Huebscher U.
      Gene 134:191-200(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: BALB/c.
    2. "Mouse DNA polymerase delta gene (Pold1) maps to chromosome 7."
      Goldsby R.E., Singh M., Preston B.D.
      Mamm. Genome 9:92-93(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 129/SvJ.
    3. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: C57BL/6J.
      Tissue: Heart and Liver.
    4. Lubec G., Sunyer B., Chen W.-Q.
      Submitted (JAN-2009) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 408-415, IDENTIFICATION BY MASS SPECTROMETRY.
      Strain: OF1.
      Tissue: Hippocampus.

    Entry informationi

    Entry nameiDPOD1_MOUSE
    AccessioniPrimary (citable) accession number: P52431
    Secondary accession number(s): O54883, Q3TFX6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: July 27, 2011
    Last modified: October 1, 2014
    This is version 122 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata 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, Direct protein sequencing, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3