EC 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase
Reaction catalysed:
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Systematic name:
DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase
Alternative Name(s):
- AP endonuclease class I
- AP lyase
- AP site-DNA 5'-phosphomonoester-lyase
- Deoxyribonuclease (apurinic or apyrimidinic)
- E. coli endonuclease III
- E.coli endonuclease III
- Endodeoxyribonuclease (apurinic or apyrimidinic)
- Micrococcus luteus UV endonuclease
- Phage-T(4) UV endonuclease
- Phage-T4 UV endonuclease
- X-ray endonuclease III
EC 2.7.7.7: DNA-directed DNA polymerase
Reaction catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Systematic name:
Deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed)
Alternative Name(s):
- DNA duplicase
- DNA nucleotidyltransferase
- DNA nucleotidyltransferase (DNA-directed)
- DNA polymerase
- DNA polymerase I
- DNA polymerase II
- DNA polymerase III
- DNA polymerase alpha
- DNA polymerase beta
- DNA polymerase gamma
- DNA replicase
- DNA-dependent DNA polymerase
- Deoxynucleate polymerase
- Deoxyribonucleate nucleotidyltransferase
- Deoxyribonucleic acid duplicase
- Deoxyribonucleic acid polymerase
- Deoxyribonucleic duplicase
- Deoxyribonucleic polymerase
- Deoxyribonucleic polymerase I
- Duplicase
- Klenow fragment
- Sequenase
- Taq DNA polymerase
- Taq Pol I
- Tca DNA polymerase
GO terms
Biochemical function:
- class I DNA-(apurinic or apyrimidinic site) endonuclease activity
- 5'-deoxyribose-5-phosphate lyase activity
- metal ion binding
- DNA polymerase activity
- enzyme binding
- lyase activity
- nucleotidyltransferase activity
- transferase activity
- microtubule binding
- protein binding
- DNA-(apurinic or apyrimidinic site) endonuclease activity
- DNA-directed DNA polymerase activity
- damaged DNA binding
- DNA binding
Biological process:
- DNA biosynthetic process
- immunoglobulin heavy chain V-D-J recombination
- response to hyperoxia
- neuron apoptotic process
- homeostasis of number of cells
- spleen development
- lymph node development
- response to ethanol
- somatic hypermutation of immunoglobulin genes
- somatic diversification of immunoglobulins
- response to gamma radiation
- macromolecule biosynthetic process
- intrinsic apoptotic signaling pathway in response to DNA damage
- salivary gland morphogenesis
- DNA damage response
- inflammatory response
- apoptotic process
- double-strand break repair via nonhomologous end joining
- nucleotide-excision repair, DNA gap filling
- pyrimidine dimer repair
- base-excision repair, gap-filling
- base-excision repair
- DNA repair
- DNA-templated DNA replication
- DNA replication
- DNA metabolic process
- in utero embryonic development
Cellular component:
Sequence families
Protein families (Pfam)
![The deposited structure of PDB entry 1zqo contains 1 copy of Pfam domain PF14791 (DNA polymerase beta thumb) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_Pfam_PF14791_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of Pfam domain <span class='highlight'>PF14791 (DNA polymerase beta thumb)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")
![The deposited structure of PDB entry 1zqo contains 1 copy of Pfam domain PF14792 (DNA polymerase beta palm) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_Pfam_PF14792_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of Pfam domain <span class='highlight'>PF14792 (DNA polymerase beta palm)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")
![The deposited structure of PDB entry 1zqo contains 1 copy of Pfam domain PF10391 (Fingers domain of DNA polymerase lambda) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_Pfam_PF10391_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of Pfam domain <span class='highlight'>PF10391 (Fingers domain of DNA polymerase lambda)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")
![The deposited structure of PDB entry 1zqo contains 1 copy of Pfam domain PF14716 (Helix-hairpin-helix domain) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_Pfam_PF14716_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of Pfam domain <span class='highlight'>PF14716 (Helix-hairpin-helix domain)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")
InterPro annotations
Structure domains
CATH domains
3.30.210.10
Class:
Alpha Beta
Architecture:
2-Layer Sandwich
Topology:
Beta Polymerase; domain 3
Homology:
DNA polymerase, thumb domain
Occurring in:
![The deposited structure of PDB entry 1zqo contains 1 copy of CATH domain 3.30.210.10 (Beta Polymerase; domain 3) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_CATH_3.30.210.10_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of CATH domain <span class='highlight'>3.30.210.10 (Beta Polymerase; domain 3)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")
3.30.460.10
Class:
Alpha Beta
Architecture:
2-Layer Sandwich
Topology:
Beta Polymerase; domain 2
Homology:
Beta Polymerase, domain 2
Occurring in:
![The deposited structure of PDB entry 1zqo contains 1 copy of CATH domain 3.30.460.10 (Beta Polymerase; domain 2) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_CATH_3.30.460.10_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of CATH domain <span class='highlight'>3.30.460.10 (Beta Polymerase; domain 2)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")
1.10.150.20
Class:
Mainly Alpha
Architecture:
Orthogonal Bundle
Topology:
DNA polymerase; domain 1
Homology:
5' to 3' exonuclease, C-terminal subdomain
Occurring in:
![The deposited structure of PDB entry 1zqo contains 1 copy of CATH domain 1.10.150.20 (DNA polymerase; domain 1) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_CATH_1.10.150.20_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of CATH domain <span class='highlight'>1.10.150.20 (DNA polymerase; domain 1)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")
![The deposited structure of PDB entry 1zqo contains 1 copy of CATH domain 1.10.150.110 (DNA polymerase; domain 1) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_CATH_1.10.150.110_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of CATH domain <span class='highlight'>1.10.150.110 (DNA polymerase; domain 1)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")
SCOP annotations
81300
Class:
Alpha and beta proteins (a+b)
Fold:
Nucleotidyltransferase
Superfamily:
Nucleotidyltransferase
Occurring in:
![The deposited structure of PDB entry 1zqo contains 1 copy of SCOP domain 81300 (DNA polymerase beta-like) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_SCOP_81300_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of SCOP domain <span class='highlight'>81300 (DNA polymerase beta-like)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")
81584
Class:
All alpha proteins
Fold:
SAM domain-like
Superfamily:
PsbU/PolX domain-like
Occurring in:
![The deposited structure of PDB entry 1zqo contains 1 copy of SCOP domain 81584 (DNA polymerase beta-like, second domain) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_SCOP_81584_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of SCOP domain <span class='highlight'>81584 (DNA polymerase beta-like, second domain)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")
47803
Class:
All alpha proteins
Fold:
SAM domain-like
Superfamily:
DNA polymerase beta, N-terminal domain-like
Occurring in:
![The deposited structure of PDB entry 1zqo contains 1 copy of SCOP domain 47803 (DNA polymerase beta, N-terminal domain-like) in DNA polymerase beta. Showing 1 copy in chain C [auth A].](https://www.ebi.ac.uk/pdbe/static/entry/1zqo_3_A_SCOP_47803_image-200x200.png "The deposited structure of PDB entry <span class='highlight'>1zqo</span> contains 1 copy of SCOP domain <span class='highlight'>47803 (DNA polymerase beta, N-terminal domain-like)</span> in <span class='highlight'>DNA polymerase beta</span>. Showing 1 copy in chain <span class='highlight'>C [auth A]</span>.")