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P06766 (DPOLB_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 149. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA polymerase beta

EC=2.7.7.7
EC=4.2.99.-
Gene names
Name:Polb
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length335 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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.

Catalytic activity

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

Cofactor

Binds 2 magnesium ions per subunit.

Subunit structure

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

Subcellular location

Nucleus. Cytoplasm By similarity. Note: Cytoplasmic in normal conditions. Translocates to the nucleus following DNA damage By similarity.

Domain

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

Post-translational modification

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.

Sequence similarities

Belongs to the DNA polymerase type-X family.

Ontologies

Keywords
   Biological processDNA damage
DNA repair
DNA replication
DNA synthesis
   Cellular componentCytoplasm
Nucleus
   LigandDNA-binding
Magnesium
Metal-binding
Sodium
   Molecular functionDNA-directed DNA polymerase
Lyase
Nucleotidyltransferase
Transferase
   PTMAcetylation
Isopeptide bond
Methylation
Ubl conjugation
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processDNA biosynthetic process

Inferred from mutant phenotype PubMed 9099618. Source: RGD

DNA-dependent DNA replication

Inferred from direct assay PubMed 17412650. Source: GOC

base-excision repair

Inferred from sequence or structural similarity. Source: UniProtKB

base-excision repair, gap-filling

Inferred from direct assay PubMed 17412650. Source: RGD

cellular response to DNA damage stimulus

Inferred from sequence or structural similarity. Source: UniProtKB

intrinsic apoptotic signaling pathway in response to DNA damage

Inferred from electronic annotation. Source: Ensembl

neuron apoptotic process

Inferred from electronic annotation. Source: Ensembl

pyrimidine dimer repair

Inferred from direct assay PubMed 12388548. Source: RGD

response to ethanol

Inferred from expression pattern PubMed 18259862. Source: RGD

   Cellular_componentcytoplasm

Inferred from sequence or structural similarity. Source: UniProtKB

nucleus

Inferred from direct assay PubMed 17412650PubMed 967678. Source: RGD

spindle microtubule

Inferred from electronic annotation. Source: Ensembl

   Molecular_functionDNA binding

Inferred from direct assay Ref.13. Source: UniProtKB

DNA-directed DNA polymerase activity

Inferred from sequence or structural similarity. Source: UniProtKB

damaged DNA binding

Inferred from direct assay PubMed 12388548. Source: RGD

lyase activity

Inferred from sequence or structural similarity. Source: UniProtKB

metal ion binding

Inferred from direct assay Ref.13. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 335335DNA polymerase beta
PRO_0000218780

Regions

Region183 – 19210DNA binding

Sites

Active site721Schiff-base intermediate with DNA By similarity
Metal binding1011Sodium; via carbonyl oxygen
Metal binding1031Sodium; via carbonyl oxygen
Metal binding1061Sodium; via carbonyl oxygen
Metal binding1901Magnesium 1
Metal binding1901Magnesium 2
Metal binding1921Magnesium 1
Metal binding1921Magnesium 2
Metal binding2561Magnesium 2

Amino acid modifications

Modified residue721N6-acetyllysine By similarity
Modified residue831Omega-N-methylarginine; by PRMT6 By similarity
Modified residue1521Omega-N-methylarginine; by PRMT6 By similarity
Cross-link41Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity
Cross-link61Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity
Cross-link81Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity

Experimental info

Mutagenesis1901D → E or S: Loss of activity. Ref.7
Mutagenesis1911M → I: No loss of activity.
Mutagenesis1911M → T: 50% loss of activity.
Mutagenesis1921D → E or S: Loss of activity. Ref.7
Mutagenesis2461D → V: Misincorporates T nucleotide opposite G/C template. Ref.9
Sequence conflict2281L → R in AAA41901. Ref.1
Sequence conflict2281L → R in AAB00389. Ref.2
Sequence conflict2281L → R in AAA41900. Ref.4

Secondary structure

................................................................ 335
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P06766 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: BBF8498C0D3FBFC9

FASTA33538,327
        10         20         30         40         50         60 
MSKRKAPQET LNGGITDMLV ELANFEKNVS QAIHKYNAYR KAASVIAKYP HKIKSGAEAK 

        70         80         90        100        110        120 
KLPGVGTKIA EKIDEFLATG KLRKLEKIRQ DDTSSSINFL TRVTGIGPSA ARKLVDEGIK 

       130        140        150        160        170        180 
TLEDLRKNED KLNHHQRIGL KYFEDFEKRI PREEMLQMQD IVLNEVKKLD PEYIATVCGS 

       190        200        210        220        230        240 
FRRGAESSGD MDVLLTHPNF TSESSKQPKL LHRVVEQLQK VRFITDTLSK GETKFMGVCQ 

       250        260        270        280        290        300 
LPSENDENEY PHRRIDIRLI PKDQYYCGVL YFTGSDIFNK NMRAHALEKG FTINEYTIRP 

       310        320        330 
LGVTGVAGEP LPVDSEQDIF DYIQWRYREP KDRSE 

« Hide

References

« Hide 'large scale' references
[1]"Homology between mammalian DNA polymerase beta and terminal deoxynucleotidyltransferase."
Matsukage A., Nishikawa K., Ooi T., Seto Y., Yamaguchi M.
J. Biol. Chem. 262:8960-8962(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]Konopinski R., Nowak R., Siedlecki J.A.
Submitted (OCT-1995) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Strain: Wistar.
[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: Thymus.
[4]"Structure of rat DNA polymerase beta revealed by partial amino acid sequencing and cDNA cloning."
Zmudzka B.Z., Sengupta D., Matsukage A., Cobianchi F., Kumar P., Wilson S.H.
Proc. Natl. Acad. Sci. U.S.A. 83:5106-5110(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 18-335.
[5]"Studies of the domain structure of mammalian DNA polymerase beta. Identification of a discrete template binding domain."
Kumar P., Widen S.G., Williams K.R., Kedar P., Karpel R.L., Wilson S.H.
J. Biol. Chem. 265:2124-2131(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: PARTIAL PROTEIN SEQUENCE, SEQUENCE REVISION TO 228.
[6]"Site-directed mutagenesis of recombinant rat DNA polymerase beta: involvement of arginine-183 in primer recognition."
Date T., Yamamoto S., Tanihara K., Nishimoto Y., Liu N., Matsukage A.
Biochemistry 29:5027-5034(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: IMPORTANCE OF ARG-183 IN PRIMER BINDING.
[7]"Aspartic acid residues at positions 190 and 192 of rat DNA polymerase beta are involved in primer binding."
Date T., Yamamoto S., Tanihara K., Nishimoto Y., Matsukage A.
Biochemistry 30:5286-5292(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF ASP-190 AND ASP-192, IMPORTANCE OF ASP-190 AND ASP-192 IN PRIMER BINDING.
[8]"Mammalian DNA polymerase beta: characterization of a 16-kDa transdomain fragment containing the nucleic acid-binding activities of the native enzyme."
Casas-Finet J.R., Kumar A., Karpel R.L., Wilson S.H.
Biochemistry 31:10272-10280(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: DNA-BINDING REGION.
[9]"The D246V mutant of DNA polymerase beta misincorporates nucleotides: evidence for a role for the flexible loop in DNA positioning within the active site."
Dalal S., Kosa J.L., Sweasy J.B.
J. Biol. Chem. 279:577-584(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF ASP-246, IMPORTANCE OF ASP-246 IN FIDELITY.
[10]"2.3-A crystal structure of the catalytic domain of DNA polymerase beta."
Davies J.F. II, Almassy R.J., Hostomska Z., Ferre R.A., Hostomsky Z.
Cell 76:1123-1133(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[11]"Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism."
Sawaya M.R., Pelletier H., Kumar A., Wilson S.H., Kraut J.
Science 264:1930-1935(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[12]"Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis."
Pelletier H., Sawaya M.R.
Biochemistry 35:12778-12787(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
[13]"Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes."
Arndt J.W., Gong W., Zhong X., Showalter A.K., Liu J., Dunlap C.A., Lin Z., Paxson C., Tsai M.-D., Chan M.K.
Biochemistry 40:5368-5375(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
[14]"Three-dimensional solution structure of the N-terminal domain of DNA polymerase beta and mapping of the ssDNA interaction interface."
Liu D., Prasad R., Wilson S.H., DeRose E.F., Mullen G.P.
Biochemistry 35:6188-6200(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-87.
[15]"Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase beta. Correlation with DNA binding and dRP lyase activity."
Maciejewski M.W., Liu D., Prasad R., Wilson S.H., Mullen G.P.
J. Mol. Biol. 296:229-253(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-87.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J02776 mRNA. Translation: AAA41901.1.
U38801 mRNA. Translation: AAB00389.1.
BC098668 mRNA. Translation: AAH98668.1.
M13961 mRNA. Translation: AAA41900.1.
PIRA27112.
RefSeqNP_058837.2. NM_017141.2.
UniGeneRn.9346.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1BNONMR-A1-87[»]
1BNPNMR-A1-87[»]
1BPBX-ray2.30A88-335[»]
1BPDX-ray3.60A1-335[»]
1BPEX-ray2.90A1-335[»]
1DK2NMR-A2-87[»]
1DK3NMR-A1-87[»]
1HUOX-ray2.60A/B1-335[»]
1HUZX-ray2.60A/B1-335[»]
1JN3X-ray2.35A85-335[»]
1NOMX-ray3.00A88-335[»]
1RPLX-ray2.30A85-335[»]
1ZQUX-ray2.60A88-335[»]
1ZQVX-ray2.70A88-335[»]
1ZQWX-ray2.30A88-335[»]
1ZQXX-ray2.50A88-335[»]
1ZQYX-ray2.30A88-335[»]
1ZQZX-ray2.70A88-335[»]
2BPCX-ray2.80A88-335[»]
2BPFX-ray2.90A1-335[»]
2BPGX-ray3.60A/B1-335[»]
2VANX-ray2.10A91-335[»]
3K75X-ray2.95D/E91-335[»]
3LQCX-ray2.35B142-335[»]
3UXNX-ray2.50A/B1-335[»]
3UXOX-ray2.10A/B1-335[»]
3UXPX-ray2.72A/B1-335[»]
3V72X-ray2.49A1-335[»]
3V7JX-ray2.25A4-335[»]
3V7KX-ray2.27A4-335[»]
3V7LX-ray2.66A4-335[»]
ProteinModelPortalP06766.
SMRP06766. Positions 10-334.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-44707N.
MINTMINT-1504350.

Chemistry

BindingDBP06766.
ChEMBLCHEMBL4343.

PTM databases

PhosphoSiteP06766.

Proteomic databases

PaxDbP06766.
PRIDEP06766.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000026039; ENSRNOP00000026039; ENSRNOG00000019150.
GeneID29240.
KEGGrno:29240.
UCSCRGD:3363. rat.

Organism-specific databases

CTD5423.
RGD3363. Polb.

Phylogenomic databases

eggNOGCOG1796.
GeneTreeENSGT00530000063002.
HOGENOMHOG000007787.
HOVERGENHBG002359.
InParanoidP06766.
KOK02330.
OMARYREPKD.
OrthoDBEOG7RJPRK.
PhylomeDBP06766.
TreeFamTF103002.

Gene expression databases

GenevestigatorP06766.

Family and domain databases

Gene3D1.10.8.310. 1 hit.
InterProIPR002054. 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.
[Graphical view]
PfamPF14792. DNA_pol_B_palm. 1 hit.
PF10391. DNA_pol_lambd_f. 1 hit.
[Graphical view]
PRINTSPR00869. DNAPOLX.
PR00870. DNAPOLXBETA.
SMARTSM00278. HhH1. 2 hits.
SM00483. POLXc. 1 hit.
[Graphical view]
SUPFAMSSF47802. SSF47802. 1 hit.
SSF81585. SSF81585. 1 hit.
PROSITEPS00522. DNA_POLYMERASE_X. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP06766.
NextBio608510.
PROP06766.

Entry information

Entry nameDPOLB_RAT
AccessionPrimary (citable) accession number: P06766
Secondary accession number(s): Q4G081
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 149 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references