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DNA polymerase beta (EC 2.7.7.7) (EC 4.2.99.-)

 DPOLB_MOUSE             Reviewed;         335 AA.
Q8K409; Q3UAB6; Q922Z7;
07-JUN-2004, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
12-SEP-2018, entry version 147.
RecName: Full=DNA polymerase beta;
EC=2.7.7.7;
EC=4.2.99.-;
Name=Polb;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090 {ECO:0000312|EMBL:AAM49616.1};
[1] {ECO:0000312|EMBL:AAM49616.1}
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=129/Ola {ECO:0000312|EMBL:AAM49616.1};
Poltoratsky V.P., Wilson S.H.;
"Sequence of mouse DNA polymerase beta.";
Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=C57BL/6J; TISSUE=Amnion, Bone marrow, and Testis;
PubMed=16141072; DOI=10.1126/science.1112014;
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.;
"The transcriptional landscape of the mammalian genome.";
Science 309:1559-1563(2005).
[3] {ECO:0000305}
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Mammary gland, and Testis {ECO:0000312|EMBL:AAH60998.1};
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[4]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Spleen, and Testis;
PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
"A tissue-specific atlas of mouse protein phosphorylation and
expression.";
Cell 143:1174-1189(2010).
[5]
ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-72, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Embryonic fibroblast;
PubMed=23806337; DOI=10.1016/j.molcel.2013.06.001;
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.;
"SIRT5-mediated lysine desuccinylation impacts diverse metabolic
pathways.";
Mol. Cell 50:919-930(2013).
-!- FUNCTION: 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). {ECO:0000250}.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1).
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000250|UniProtKB:P06766};
Note=Binds 2 magnesium ions per subunit.
{ECO:0000250|UniProtKB:P06766};
-!- SUBUNIT: Monomer. Interacts with APEX1, HUWE1/ARF-BP1, STUB1/CHIP
and USP47 (By similarity). Interacts with FAM168A (By similarity).
{ECO:0000250|UniProtKB:P06746}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Cytoplasm
{ECO:0000250}. Note=Cytoplasmic in normal conditions. Translocates
to the nucleus following DNA damage (By similarity).
{ECO:0000250}.
-!- DOMAIN: Residues 239-252 form a flexible loop which appears to
affect the polymerase fidelity. {ECO:0000250}.
-!- PTM: Methylation by PRMT6 stimulates the polymerase activity by
enhancing DNA binding and processivity. {ECO:0000250}.
-!- PTM: 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). {ECO:0000250}.
-!- SIMILARITY: Belongs to the DNA polymerase type-X family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAH06681.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; AF513911; AAM49616.1; -; mRNA.
EMBL; AK077127; BAC36630.1; -; mRNA.
EMBL; AK146745; BAE27405.1; -; mRNA.
EMBL; AK151436; BAE30399.1; -; mRNA.
EMBL; BC006681; AAH06681.1; ALT_SEQ; mRNA.
EMBL; BC060998; AAH60998.1; -; mRNA.
CCDS; CCDS22181.1; -.
RefSeq; NP_035260.1; NM_011130.2.
UniGene; Mm.123211; -.
UniGene; Mm.473777; -.
ProteinModelPortal; Q8K409; -.
SMR; Q8K409; -.
BioGrid; 202289; 3.
IntAct; Q8K409; 2.
MINT; Q8K409; -.
STRING; 10090.ENSMUSP00000033938; -.
BindingDB; Q8K409; -.
ChEMBL; CHEMBL4565; -.
iPTMnet; Q8K409; -.
PhosphoSitePlus; Q8K409; -.
EPD; Q8K409; -.
MaxQB; Q8K409; -.
PaxDb; Q8K409; -.
PeptideAtlas; Q8K409; -.
PRIDE; Q8K409; -.
Ensembl; ENSMUST00000033938; ENSMUSP00000033938; ENSMUSG00000031536.
GeneID; 18970; -.
KEGG; mmu:18970; -.
UCSC; uc009ldk.2; mouse.
CTD; 5423; -.
MGI; MGI:97740; Polb.
eggNOG; KOG2534; Eukaryota.
eggNOG; COG1796; LUCA.
GeneTree; ENSGT00530000063002; -.
HOGENOM; HOG000007787; -.
HOVERGEN; HBG002359; -.
InParanoid; Q8K409; -.
KO; K02330; -.
OMA; DLFNKNM; -.
OrthoDB; EOG091G0HMG; -.
PhylomeDB; Q8K409; -.
TreeFam; TF103002; -.
Reactome; R-MMU-110362; POLB-Dependent Long Patch Base Excision Repair.
Reactome; R-MMU-110373; Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
Reactome; R-MMU-110381; Resolution of AP sites via the single-nucleotide replacement pathway.
Reactome; R-MMU-5649702; APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway.
Reactome; R-MMU-5651801; PCNA-Dependent Long Patch Base Excision Repair.
Reactome; R-MMU-5689880; Ub-specific processing proteases.
Reactome; R-MMU-73930; Abasic sugar-phosphate removal via the single-nucleotide replacement pathway.
ChiTaRS; Polb; mouse.
PRO; PR:Q8K409; -.
Proteomes; UP000000589; Chromosome 8.
Bgee; ENSMUSG00000031536; Expressed in 299 organ(s), highest expression level in testis.
CleanEx; MM_POLB; -.
ExpressionAtlas; Q8K409; baseline and differential.
Genevisible; Q8K409; MM.
GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
GO; GO:0005874; C:microtubule; ISO:MGI.
GO; GO:0005634; C:nucleus; ISO:MGI.
GO; GO:0032991; C:protein-containing complex; ISO:MGI.
GO; GO:0005876; C:spindle microtubule; ISO:MGI.
GO; GO:0000795; C:synaptonemal complex; TAS:MGI.
GO; GO:0003684; F:damaged DNA binding; ISO:MGI.
GO; GO:0003677; F:DNA binding; ISO:MGI.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; ISS:UniProtKB.
GO; GO:0019899; F:enzyme binding; ISO:MGI.
GO; GO:0016829; F:lyase activity; ISS:UniProtKB.
GO; GO:0046872; F:metal ion binding; ISO:MGI.
GO; GO:0008017; F:microtubule binding; ISO:MGI.
GO; GO:0007568; P:aging; IEA:Ensembl.
GO; GO:0006915; P:apoptotic process; IMP:MGI.
GO; GO:0006284; P:base-excision repair; ISS:UniProtKB.
GO; GO:0006287; P:base-excision repair, gap-filling; IMP:MGI.
GO; GO:0006974; P:cellular response to DNA damage stimulus; ISS:UniProtKB.
GO; GO:0071897; P:DNA biosynthetic process; ISO:MGI.
GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
GO; GO:0048872; P:homeostasis of number of cells; IMP:MGI.
GO; GO:0071707; P:immunoglobulin heavy chain V-D-J recombination; IMP:MGI.
GO; GO:0006954; P:inflammatory response; IMP:MGI.
GO; GO:0008630; P:intrinsic apoptotic signaling pathway in response to DNA damage; IMP:MGI.
GO; GO:0048535; P:lymph node development; IMP:MGI.
GO; GO:0051402; P:neuron apoptotic process; IGI:MGI.
GO; GO:0006290; P:pyrimidine dimer repair; ISO:MGI.
GO; GO:0045471; P:response to ethanol; IEA:Ensembl.
GO; GO:0010332; P:response to gamma radiation; IEA:Ensembl.
GO; GO:0055093; P:response to hyperoxia; IEA:Ensembl.
GO; GO:0007435; P:salivary gland morphogenesis; IMP:MGI.
GO; GO:0016445; P:somatic diversification of immunoglobulins; IMP:MGI.
GO; GO:0016446; P:somatic hypermutation of immunoglobulin genes; IMP:MGI.
GO; GO:0048536; P:spleen development; IMP:MGI.
CDD; cd00141; NT_POLXc; 1.
Gene3D; 1.10.150.110; -; 1.
Gene3D; 3.30.210.10; -; 1.
InterPro; IPR002054; DNA-dir_DNA_pol_X.
InterPro; IPR019843; DNA_pol-X_BS.
InterPro; IPR010996; DNA_pol_b-like_N.
InterPro; IPR028207; DNA_pol_B_palm_palm.
InterPro; IPR018944; DNA_pol_lambd_fingers_domain.
InterPro; IPR027421; DNA_pol_lamdba_lyase_dom_sf.
InterPro; IPR037160; DNA_Pol_thumb_sf.
InterPro; IPR022312; DNA_pol_X.
InterPro; IPR002008; DNA_pol_X_beta-like.
InterPro; IPR003583; Hlx-hairpin-Hlx_DNA-bd_motif.
InterPro; IPR029398; PolB_thumb.
Pfam; PF14792; DNA_pol_B_palm; 1.
Pfam; PF14791; DNA_pol_B_thumb; 1.
Pfam; PF10391; DNA_pol_lambd_f; 1.
Pfam; PF14716; HHH_8; 1.
PRINTS; PR00869; DNAPOLX.
PRINTS; PR00870; DNAPOLXBETA.
SMART; SM00278; HhH1; 2.
SMART; SM00483; POLXc; 1.
SUPFAM; SSF47802; SSF47802; 1.
PROSITE; PS00522; DNA_POLYMERASE_X; 1.
1: Evidence at protein level;
Acetylation; Complete proteome; Cytoplasm; DNA damage; DNA repair;
DNA replication; DNA synthesis; DNA-binding;
DNA-directed DNA polymerase; Isopeptide bond; Lyase; Magnesium;
Metal-binding; Methylation; Nucleotidyltransferase; Nucleus;
Reference proteome; Sodium; Transferase; Ubl conjugation.
CHAIN 1 335 DNA polymerase beta.
/FTId=PRO_0000218779.
REGION 183 192 DNA binding. {ECO:0000250}.
ACT_SITE 72 72 Schiff-base intermediate with DNA.
{ECO:0000250}.
METAL 101 101 Sodium; via carbonyl oxygen.
{ECO:0000250}.
METAL 103 103 Sodium; via carbonyl oxygen.
{ECO:0000250}.
METAL 106 106 Sodium; via carbonyl oxygen.
{ECO:0000250}.
METAL 190 190 Magnesium 1. {ECO:0000250}.
METAL 190 190 Magnesium 2. {ECO:0000250}.
METAL 192 192 Magnesium 1. {ECO:0000250}.
METAL 192 192 Magnesium 2. {ECO:0000250}.
METAL 256 256 Magnesium 2. {ECO:0000250}.
MOD_RES 72 72 N6-acetyllysine.
{ECO:0000244|PubMed:23806337}.
MOD_RES 83 83 Omega-N-methylarginine; by PRMT6.
{ECO:0000250|UniProtKB:P06746}.
MOD_RES 152 152 Omega-N-methylarginine; by PRMT6.
{ECO:0000250|UniProtKB:P06746}.
CROSSLNK 41 41 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin).
{ECO:0000250|UniProtKB:P06746}.
CROSSLNK 61 61 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin).
{ECO:0000250|UniProtKB:P06746}.
CROSSLNK 81 81 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin).
{ECO:0000250|UniProtKB:P06746}.
SEQUENCE 335 AA; 38288 MW; 41E62348DC766A39 CRC64;
MSKRKAPQET LNGGITDMLV ELANFEKNVS QAIHKYNAYR KAASVIAKYP HKIKSGAEAK
KLPGVGTKIA EKIDEFLATG KLRKLEKIRQ DDTSSSINFL TRVTGIGPSA ARKFVDEGIK
TLEDLRKNED KLNHHQRIGL KYFEDFEKRI PREEMLQMQD IVLNEIKKVD SEYIATVCGS
FRRGAESSGD MDVLLTHPNF TSESSKQPKL LHRVVEQLQK VHFITDTLSK GETKFMGVCQ
LPSEKDGKEY PHRRIDIRLI PKDQYYCGVL YFTGSDIFNK NMRAHALEKG FTINEYTIRP
LGVTGVAGEP LPVDSEQDIF DYIQWRYREP KDRSE


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