Q6DRD3 · DPOLB_DANRE
- ProteinDNA polymerase beta
- Genepolb
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids336 (go to sequence)
- Protein existenceEvidence at transcript level
- Annotation score5/5
Function
function
Repair polymerase that plays a key role in base-excision repair. During this process, the damaged base is excised by specific DNA glycosylases, the DNA backbone is nicked at the abasic site by an apurinic/apyrimidic (AP) endonuclease, and POLB removes 5'-deoxyribose-phosphate from the preincised AP site acting as a 5'-deoxyribose-phosphate lyase (5'-dRP lyase); through its DNA polymerase activity, it 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. It is also able to cleave sugar-phosphate bonds 3' to an intact AP site, acting as an AP lyase.
Catalytic activity
- a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)
- a 5'-end 2'-deoxyribose-2'-deoxyribonucleotide-DNA = (2E,4S)-4-hydroxypenten-2-al-5-phosphate + a 5'-end 5'-phospho-2'-deoxyribonucleoside-DNA + H+
Cofactor
Note: Binds 2 magnesium ions per subunit.
Features
Showing features for binding site, active site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 59 | K+ 1 (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 59 | Na+ 1 (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 61 | K+ 1 (UniProtKB | ChEBI) | ||||
Sequence: L | ||||||
Binding site | 61 | Na+ 1 (UniProtKB | ChEBI) | ||||
Sequence: L | ||||||
Binding site | 64 | K+ 1 (UniProtKB | ChEBI) | ||||
Sequence: V | ||||||
Binding site | 64 | Na+ 1 (UniProtKB | ChEBI) | ||||
Sequence: V | ||||||
Active site | 71 | Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity | ||||
Sequence: K | ||||||
Binding site | 100 | K+ 2 (UniProtKB | ChEBI) | ||||
Sequence: T | ||||||
Binding site | 100 | Na+ 2 (UniProtKB | ChEBI) | ||||
Sequence: T | ||||||
Binding site | 102 | K+ 2 (UniProtKB | ChEBI) | ||||
Sequence: V | ||||||
Binding site | 102 | Na+ 2 (UniProtKB | ChEBI) | ||||
Sequence: V | ||||||
Binding site | 105 | K+ 2 (UniProtKB | ChEBI) | ||||
Sequence: I | ||||||
Binding site | 105 | Na+ 2 (UniProtKB | ChEBI) | ||||
Sequence: I | ||||||
Binding site | 148 | a 2'-deoxyribonucleoside 5'-triphosphate (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Binding site | 179 | a 2'-deoxyribonucleoside 5'-triphosphate (UniProtKB | ChEBI) | ||||
Sequence: S | ||||||
Binding site | 182 | a 2'-deoxyribonucleoside 5'-triphosphate (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Binding site | 188 | a 2'-deoxyribonucleoside 5'-triphosphate (UniProtKB | ChEBI) | ||||
Sequence: G | ||||||
Binding site | 189 | a 2'-deoxyribonucleoside 5'-triphosphate (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 189 | Mg2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 189 | Mg2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 191 | Mg2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 191 | Mg2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 257 | Mg2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: D |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytoplasm | |
Cellular Component | nucleus | |
Molecular Function | class I DNA-(apurinic or apyrimidinic site) endonuclease activity | |
Molecular Function | DNA binding | |
Molecular Function | DNA-directed DNA polymerase activity | |
Molecular Function | lyase activity | |
Molecular Function | metal ion binding | |
Biological Process | base-excision repair | |
Biological Process | DNA damage response | |
Biological Process | DNA replication | |
Biological Process | double-strand break repair via nonhomologous end joining |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameDNA polymerase beta
- EC number
- Alternative names
Gene names
Organism names
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Actinopterygii > Neopterygii > Teleostei > Ostariophysi > Cypriniformes > Danionidae > Danioninae > Danio
Accessions
- Primary accessionQ6DRD3
Proteomes
Organism-specific databases
PTM/Processing
Features
Showing features for chain, modified residue.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000218781 | 1-336 | DNA polymerase beta | |||
Sequence: SKRKAPQESLNEGITDFLVELANYERNVNRAIHKYNAYRKAASVIAKYPQKIKSGTEAKKLDGVGAKIAEKIDEFLTTGKLRKLEKIRNDDTSSSINFLTRVTGIGPAAARKFFDEGVRNLEDLKKIEHKLNHHQQIGLKYFEEFEKRIPRSEMQKMEALILKELDIVDPEYIGTICGSYRRGAESSGDIDILLTHPDFTSQSEKQPKLLHAVVDHLESIGFITDTLSKGDTKFMGVCQLQKEKEEEEEESLHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRTHALEKGFTLNEYTIRPLGVTGVAGEPLLVDSEKDIFEYIQWKYREPKDRSE | ||||||
Modified residue | 82 | Omega-N-methylarginine; by PRMT6 | ||||
Sequence: R | ||||||
Modified residue | 151 | Omega-N-methylarginine; by PRMT6 | ||||
Sequence: R |
Post-translational modification
Methylation by PRMT6 stimulates the polymerase activity by enhancing DNA binding and processivity.
Ubiquitinated: 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).
Keywords
- PTM
Proteomic databases
Interaction
Protein-protein interaction databases
Structure
Family & Domains
Sequence
- Sequence statusComplete
- Length336
- Mass (Da)38,566
- Last updated2005-09-13 v2
- ChecksumFDF6EA3088354973
Computationally mapped potential isoform sequences
There is 1 potential isoform mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
B0R194 | B0R194_DANRE | polb | 339 |
Keywords
- Technical term