PDBsum entry 6e3v

DNA binding protein/DNA

PDB id: 6e3v

Contents

Protein chain

326 a.a.

DNA/RNA

Ligands

1FZ

Metals

_MG ×2

_NA ×2

Waters ×196

PDB id:

6e3v

Name:

DNA binding protein/DNA

Title:

Structure of human DNA polymerase beta complexed with 8oa in the template base paired with incoming non-hydrolyzable ttp

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. DNA (5'-d( Cp Cp Gp Ap Cp (A38) p Tp Cp Gp Cp Ap Tp Cp Ap Gp C)-3'). Chain: t. Engineered: yes. DNA (5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp A)-3'). Chain: p.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606

Resolution:

1.96Å R-factor: 0.197 R-free: 0.240

Authors:

M.-C.Koag,S.Lee

Key ref:

M.C.Koag et al. (2019). Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases. J Am Chem Soc, 141, 4584-4596. PubMed id: 30817143 DOI: 10.1021/jacs.8b08551

Date:

15-Jul-18 Release date: 03-Apr-19

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 326 a.a.

DNA/RNA chains

C-C-G-A-C-A38-T-C-G-C-A-T-C-A-G-C 16 bases

G-C-T-G-A-T-G-C-G-A 10 bases

G-T-C-G-G 5 bases

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: E.C.4.2.99.- - ?????
• Enzyme class 3: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/jacs.8b08551

J Am Chem Soc 141:4584-4596 (2019)

PubMed id: 30817143

Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases.

M.C.Koag, H.Jung, S.Lee.

ABSTRACT

Reactive oxygen species attack DNA to produce 7,8-dihyro-8-oxoguanine (oxoG) and 7,8-dihydro-8-oxoadenine (oxoA) as major lesions. The structural basis for the mutagenicity of oxoG, which induces G to T mutations, is well understood. However, the structural basis for the mutagenic potential of oxoA, which induces A to C mutations, remains poorly understood. To gain insight into oxoA-induced mutagenesis, we conducted kinetic studies of human DNA polymerases β and η replicating across oxoA and structural studies of polβ incorporating dTTP/dGTP opposite oxoA. While polη readily bypassed oxoA, it incorporated dGTP opposite oxoA with a catalytic specificity comparable to that of correct insertion, underscoring the promutagenic nature of the major oxidative adenine lesion. Polη and polβ incorporated dGTP opposite oxoA ∼170-fold and ∼100-fold more efficiently than that opposite dA, respectively, indicating that the 8-oxo moiety greatly facilitated error-prone replication. Crystal structures of polβ showed that, when paired with an incoming dTTP, the templating oxoA adopted an anti conformation and formed Watson-Crick base pair. When paired with dGTP, oxoA adopted a syn conformation and formed a Hoogsteen base pair with Watson-Crick-like geometry, highlighting the dual-coding potential of oxoA. The templating oxoA was stabilized by Lys280-mediated stacking and hydrogen bonds. Overall, these results provide insight into the mutagenic potential and dual-coding nature of the major oxidative adenine lesion.