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P52431

- DPOD1_MOUSE

UniProt

P52431 - DPOD1_MOUSE

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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

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

[4Fe-4S] clusterBy similarityNote: 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
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

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.
REACT_240368. Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
REACT_245471. Polymerase switching.
REACT_246095. Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
REACT_251075. Removal of the Flap Intermediate.
REACT_259967. Leading Strand Synthesis.
REACT_262992. Processive synthesis on the lagging strand.

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. aggresome Source: Ensembl
  2. cytoplasm Source: Ensembl
  3. delta DNA polymerase complex Source: RefGenome
  4. nucleotide-excision repair complex Source: Ensembl
  5. nucleus Source: RefGenome
Complete GO annotation...

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.
ExpressionAtlasiP52431. baseline and differential.
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.
InParanoidiP52431.
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

        10         20         30         40         50
MDCKRRQGPG PGVPPKRARG HLWDEDEPSP SQFEANLALL EEIEAENRLQ
60 70 80 90 100
EAEEELQLPP EGTVGGQFST ADIDPRWRRP TLRALDPSTE PLIFQQLEID
110 120 130 140 150
HYVGSAPPLP EGPLPSRNSV PILRAFGVTD EGFSVCCHIQ GFAPYFYTPA
160 170 180 190 200
PPGFGAEHLS ELQQELNAAI SRDQRGGKEL SGPAVLAIEL CSRESMFGYH
210 220 230 240 250
GHGPSPFLRI TLALPRLMAP ARRLLEQGVR VPGLGTPSFA PYEANVDFEI
260 270 280 290 300
RFMVDADIVG CNWLELPAGK YVRRAEKKAT LCQLEVDVLW SDVISHPPEG
310 320 330 340 350
QWQRIAPLRV LSFDIECAGR KGIFPEPERD PVIQICSLGL RWGEPEPFLR
360 370 380 390 400
LALTLRPCAP ILGAKVQSYE REEDLLQAWA DFILAMDPDV ITGYNIQNFD
410 420 430 440 450
LPYLISRAQA LKVDRFPFLG RVTGLRSNIR DSSFQSRQVG RRDSKVISMV
460 470 480 490 500
GRVQMDMLQV LLREHKLRSY TLNAVSFHFL GEQKEDVQHS IITDLQNGNE
510 520 530 540 550
QTRRRLAVYC LKDAFLPLRL LERLMVLVNN VEMARVTGVP LGYLLTRGQQ
560 570 580 590 600
VKVVSQLLRQ AMRQGLLMPV VKTEGSEDYT GATVIEPLKG YYDVPIATLD
610 620 630 640 650
FSSLYPSIMM AHNLCYTTLL RPGAAQKLGL KPDEFIKTPT GDEFVKSSVR
660 670 680 690 700
KGLLPQILEN LLSARKRAKA ELAQETDPLR RQVLDGRQLA LKVSANSVYG
710 720 730 740 750
FTGAQVGKLP CLEISQSVTG FGRQMIEKTK QLVESKYTVE NGYDANAKVV
760 770 780 790 800
YGDTDSVMCR FGVSSVAEAM SLGREAANWV SSHFPSPIRL EFEKVYFPYL
810 820 830 840 850
LISKKRYAGL LFSSRSDAHD KMDCKGLEAV RRDNCPLVAN LVTSSLRRIL
860 870 880 890 900
VDRDPDGAVA HAKDVISDLL CNRIDISQLV ITKELTRAAA DYAGKQAHVE
910 920 930 940 950
LAERMRKRDP GSAPSLGDRV PYVIIGAAKG VAAYMKSEDP LFVLEHSLPI
960 970 980 990 1000
DTQYYLEQQL AKPLLRIFEP ILGEGRAESV LLRGDHTRCK TVLTSKVGGL
1010 1020 1030 1040 1050
LAFTKRRNCC IGCRSVIDHQ GAVCKFCQPR ESELYQKEVS HLNALEERFS
1060 1070 1080 1090 1100
RLWTQCQRCQ GSLHEDVICT SRDCPIFYMR KKVRKDLEDQ ERLLQRFGPP

GPEAW
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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 P52431.
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.
REACT_240368. Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
REACT_245471. Polymerase switching.
REACT_246095. Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
REACT_251075. Removal of the Flap Intermediate.
REACT_259967. Leading Strand Synthesis.
REACT_262992. Processive synthesis on the lagging strand.

Miscellaneous databases

NextBioi 295320.
PMAP-CutDB P52431.
PROi P52431.
SOURCEi Search...

Gene expression databases

Bgeei P52431.
ExpressionAtlasi P52431. baseline and differential.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 124 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