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Protein

DNA polymerase beta

Gene

Polb

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases (By similarity).By similarity

Catalytic activityi

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

Cofactori

Mg2+By similarityNote: Binds 2 magnesium ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei72 – 721Schiff-base intermediate with DNABy similarity
Metal bindingi101 – 1011Sodium; via carbonyl oxygenBy similarity
Metal bindingi103 – 1031Sodium; via carbonyl oxygenBy similarity
Metal bindingi106 – 1061Sodium; via carbonyl oxygenBy similarity
Metal bindingi190 – 1901Magnesium 1By similarity
Metal bindingi190 – 1901Magnesium 2By similarity
Metal bindingi192 – 1921Magnesium 1By similarity
Metal bindingi192 – 1921Magnesium 2By similarity
Metal bindingi256 – 2561Magnesium 2By similarity

GO - Molecular functioni

GO - Biological processi

  • aging Source: Ensembl
  • apoptotic process Source: MGI
  • base-excision repair Source: UniProtKB
  • base-excision repair, gap-filling Source: MGI
  • cellular response to DNA damage stimulus Source: UniProtKB
  • DNA replication Source: UniProtKB-KW
  • homeostasis of number of cells Source: MGI
  • immunoglobulin heavy chain V-D-J recombination Source: MGI
  • inflammatory response Source: MGI
  • intrinsic apoptotic signaling pathway in response to DNA damage Source: MGI
  • lymph node development Source: MGI
  • neuron apoptotic process Source: MGI
  • pyrimidine dimer repair Source: Ensembl
  • response to ethanol Source: Ensembl
  • response to gamma radiation Source: Ensembl
  • response to hyperoxia Source: Ensembl
  • salivary gland morphogenesis Source: MGI
  • somatic diversification of immunoglobulins Source: MGI
  • somatic hypermutation of immunoglobulin genes Source: MGI
  • spleen development Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Lyase, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA damage, DNA repair, DNA replication, DNA synthesis

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Sodium

Enzyme and pathway databases

ReactomeiR-MMU-110362. POLB-Dependent Long Patch Base Excision Repair.
R-MMU-110373. Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
R-MMU-110381. Resolution of AP sites via the single-nucleotide replacement pathway.
R-MMU-5649702. APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway.
R-MMU-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-MMU-73930. Abasic sugar-phosphate removal via the single-nucleotide replacement pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase beta (EC:2.7.7.7, EC:4.2.99.-)
Gene namesi
Name:Polb
OrganismiMus musculus (Mouse)Imported
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 8

Organism-specific databases

MGIiMGI:97740. Polb.

Subcellular locationi

  • Nucleus By similarity
  • Cytoplasm By similarity

  • Note: Cytoplasmic in normal conditions. Translocates to the nucleus following DNA damage (By similarity).By similarity

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • microtubule Source: MGI
  • nucleus Source: MGI
  • protein complex Source: MGI
  • spindle microtubule Source: MGI
  • synaptonemal complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL4565.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 335335DNA polymerase betaPRO_0000218779Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki41 – 41Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki61 – 61Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei72 – 721N6-acetyllysineCombined sources
Cross-linki81 – 81Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei83 – 831Omega-N-methylarginine; by PRMT6By similarity
Modified residuei152 – 1521Omega-N-methylarginine; by PRMT6By similarity

Post-translational modificationi

Methylation by PRMT6 stimulates the polymerase activity by enhancing DNA binding and processivity.By similarity
Ubiquitinated at Lys-41, Lys-61 and Lys-81: monoubiquitinated by HUWE1/ARF-BP1. Monoubiquitinated protein is then the target of STUB1/CHIP, which catalyzes polyubiquitination from monoubiquitin, leading to degradation by the proteasome. USP47 mediates the deubiquitination of monoubiquitinated protein, preventing polyubiquitination by STUB1/CHIP and its subsequent degradation (By similarity).By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Ubl conjugation

Proteomic databases

EPDiQ8K409.
MaxQBiQ8K409.
PaxDbiQ8K409.
PRIDEiQ8K409.

PTM databases

PhosphoSiteiQ8K409.

Expressioni

Gene expression databases

BgeeiQ8K409.
CleanExiMM_POLB.
GenevisibleiQ8K409. MM.

Interactioni

Subunit structurei

Monomer. Interacts with APEX1, HUWE1/ARF-BP1, STUB1/CHIP and USP47 (By similarity).By similarity

GO - Molecular functioni

Protein-protein interaction databases

BioGridi202289. 2 interactions.
IntActiQ8K409. 2 interactions.
MINTiMINT-4093472.
STRINGi10090.ENSMUSP00000033938.

Chemistry

BindingDBiQ8K409.

Structurei

3D structure databases

ProteinModelPortaliQ8K409.
SMRiQ8K409. Positions 1-335.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni183 – 19210DNA bindingBy similarity

Domaini

Residues 239-252 form a flexible loop which appears to affect the polymerase fidelity.By similarity

Sequence similaritiesi

Belongs to the DNA polymerase type-X family.Curated

Phylogenomic databases

eggNOGiKOG2534. Eukaryota.
COG1796. LUCA.
GeneTreeiENSGT00530000063002.
HOGENOMiHOG000007787.
HOVERGENiHBG002359.
InParanoidiQ8K409.
KOiK02330.
OMAiADYEKNV.
OrthoDBiEOG7RJPRK.
PhylomeDBiQ8K409.
TreeFamiTF103002.

Family and domain databases

Gene3Di1.10.8.310. 1 hit.
3.30.210.10. 1 hit.
InterProiIPR002054. DNA-dir_DNA_pol_X.
IPR019843. DNA_pol-X_BS.
IPR010996. DNA_pol_b-like_N.
IPR028207. DNA_pol_B_palm_palm.
IPR018944. DNA_pol_lambd_fingers_domain.
IPR022312. DNA_pol_X.
IPR002008. DNA_pol_X_beta-like.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR027420. PolB_N.
IPR029398. PolB_thumb.
[Graphical view]
PfamiPF14792. DNA_pol_B_palm. 1 hit.
PF14791. DNA_pol_B_thumb. 1 hit.
PF10391. DNA_pol_lambd_f. 1 hit.
PF14716. HHH_8. 1 hit.
[Graphical view]
PRINTSiPR00869. DNAPOLX.
PR00870. DNAPOLXBETA.
SMARTiSM00278. HhH1. 2 hits.
SM00483. POLXc. 1 hit.
[Graphical view]
SUPFAMiSSF47802. SSF47802. 1 hit.
PROSITEiPS00522. DNA_POLYMERASE_X. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8K409-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKRKAPQET LNGGITDMLV ELANFEKNVS QAIHKYNAYR KAASVIAKYP
60 70 80 90 100
HKIKSGAEAK KLPGVGTKIA EKIDEFLATG KLRKLEKIRQ DDTSSSINFL
110 120 130 140 150
TRVTGIGPSA ARKFVDEGIK TLEDLRKNED KLNHHQRIGL KYFEDFEKRI
160 170 180 190 200
PREEMLQMQD IVLNEIKKVD SEYIATVCGS FRRGAESSGD MDVLLTHPNF
210 220 230 240 250
TSESSKQPKL LHRVVEQLQK VHFITDTLSK GETKFMGVCQ LPSEKDGKEY
260 270 280 290 300
PHRRIDIRLI PKDQYYCGVL YFTGSDIFNK NMRAHALEKG FTINEYTIRP
310 320 330
LGVTGVAGEP LPVDSEQDIF DYIQWRYREP KDRSE
Length:335
Mass (Da):38,288
Last modified:January 23, 2007 - v3
Checksum:i41E62348DC766A39
GO

Sequence cautioni

The sequence AAH06681.1 differs from that shown. Reason: Frameshift at several positions. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF513911 mRNA. Translation: AAM49616.1.
AK077127 mRNA. Translation: BAC36630.1.
AK146745 mRNA. Translation: BAE27405.1.
AK151436 mRNA. Translation: BAE30399.1.
BC006681 mRNA. Translation: AAH06681.1. Sequence problems.
BC060998 mRNA. Translation: AAH60998.1.
CCDSiCCDS22181.1.
RefSeqiNP_035260.1. NM_011130.2.
UniGeneiMm.123211.
Mm.473777.

Genome annotation databases

EnsembliENSMUST00000033938; ENSMUSP00000033938; ENSMUSG00000031536.
GeneIDi18970.
KEGGimmu:18970.
UCSCiuc009ldk.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF513911 mRNA. Translation: AAM49616.1.
AK077127 mRNA. Translation: BAC36630.1.
AK146745 mRNA. Translation: BAE27405.1.
AK151436 mRNA. Translation: BAE30399.1.
BC006681 mRNA. Translation: AAH06681.1. Sequence problems.
BC060998 mRNA. Translation: AAH60998.1.
CCDSiCCDS22181.1.
RefSeqiNP_035260.1. NM_011130.2.
UniGeneiMm.123211.
Mm.473777.

3D structure databases

ProteinModelPortaliQ8K409.
SMRiQ8K409. Positions 1-335.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi202289. 2 interactions.
IntActiQ8K409. 2 interactions.
MINTiMINT-4093472.
STRINGi10090.ENSMUSP00000033938.

Chemistry

BindingDBiQ8K409.
ChEMBLiCHEMBL4565.

PTM databases

PhosphoSiteiQ8K409.

Proteomic databases

EPDiQ8K409.
MaxQBiQ8K409.
PaxDbiQ8K409.
PRIDEiQ8K409.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000033938; ENSMUSP00000033938; ENSMUSG00000031536.
GeneIDi18970.
KEGGimmu:18970.
UCSCiuc009ldk.2. mouse.

Organism-specific databases

CTDi5423.
MGIiMGI:97740. Polb.

Phylogenomic databases

eggNOGiKOG2534. Eukaryota.
COG1796. LUCA.
GeneTreeiENSGT00530000063002.
HOGENOMiHOG000007787.
HOVERGENiHBG002359.
InParanoidiQ8K409.
KOiK02330.
OMAiADYEKNV.
OrthoDBiEOG7RJPRK.
PhylomeDBiQ8K409.
TreeFamiTF103002.

Enzyme and pathway databases

ReactomeiR-MMU-110362. POLB-Dependent Long Patch Base Excision Repair.
R-MMU-110373. Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
R-MMU-110381. Resolution of AP sites via the single-nucleotide replacement pathway.
R-MMU-5649702. APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway.
R-MMU-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-MMU-73930. Abasic sugar-phosphate removal via the single-nucleotide replacement pathway.

Miscellaneous databases

ChiTaRSiPolb. mouse.
PROiQ8K409.
SOURCEiSearch...

Gene expression databases

BgeeiQ8K409.
CleanExiMM_POLB.
GenevisibleiQ8K409. MM.

Family and domain databases

Gene3Di1.10.8.310. 1 hit.
3.30.210.10. 1 hit.
InterProiIPR002054. DNA-dir_DNA_pol_X.
IPR019843. DNA_pol-X_BS.
IPR010996. DNA_pol_b-like_N.
IPR028207. DNA_pol_B_palm_palm.
IPR018944. DNA_pol_lambd_fingers_domain.
IPR022312. DNA_pol_X.
IPR002008. DNA_pol_X_beta-like.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR027420. PolB_N.
IPR029398. PolB_thumb.
[Graphical view]
PfamiPF14792. DNA_pol_B_palm. 1 hit.
PF14791. DNA_pol_B_thumb. 1 hit.
PF10391. DNA_pol_lambd_f. 1 hit.
PF14716. HHH_8. 1 hit.
[Graphical view]
PRINTSiPR00869. DNAPOLX.
PR00870. DNAPOLXBETA.
SMARTiSM00278. HhH1. 2 hits.
SM00483. POLXc. 1 hit.
[Graphical view]
SUPFAMiSSF47802. SSF47802. 1 hit.
PROSITEiPS00522. DNA_POLYMERASE_X. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence of mouse DNA polymerase beta."
    Poltoratsky V.P., Wilson S.H.
    Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: 129/OlaImported.
  2. "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: Amnion, Bone marrow and Testis.
  3. "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].
    Tissue: Mammary gland and TestisImported.
  4. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Spleen and Testis.
  5. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-72, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.

Entry informationi

Entry nameiDPOLB_MOUSE
AccessioniPrimary (citable) accession number: Q8K409
Secondary accession number(s): Q3UAB6, Q922Z7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2004
Last sequence update: January 23, 2007
Last modified: June 8, 2016
This is version 128 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, 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

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.