PDBsum entry 4o5c

Transferase, lyase/DNA

PDB id: 4o5c

Contents

Protein chain

327 a.a.

DNA/RNA

Metals

_NA ×2

Waters ×107

PDB id:

4o5c

Name:

Transferase, lyase/DNA

Title:

Structure of human DNA polymerase complexed with n7-mg as the template base in a 1-nucleotide gapped DNA

Structure:

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

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.36Å R-factor: 0.203 R-free: 0.245

Authors:

M.C.Koag,S.Lee

Key ref:

M.C.Koag et al. (2014). Transition-state destabilization reveals how human DNA polymerase β proceeds across the chemically unstable lesion N7-methylguanine. Nucleic Acids Res, 42, 8755-8766. PubMed id: 24966350 DOI: 10.1093/nar/gku554

Date:

19-Dec-13 Release date: 02-Jul-14

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 327 a.a.

DNA/RNA chains

C-C-G-A-C-FMG-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: 10.1093/nar/gku554

Nucleic Acids Res 42:8755-8766 (2014)

PubMed id: 24966350

Transition-state destabilization reveals how human DNA polymerase β proceeds across the chemically unstable lesion N7-methylguanine.

M.C.Koag, Y.Kou, H.Ouzon-Shubeita, S.Lee.

ABSTRACT

N7-Methyl-2'-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2'-fluorine-mediated transition-state destabilzation strategy. Specifically, we determined kinetic parameters for dCTP insertion opposite a chemically stable m7dG analogue, 2'-fluoro-m7dG (Fm7dG), by human DNA polymerase β (polβ) and solved three X-ray structures of polβ in complex with the templating Fm7dG paired with incoming dCTP or dTTP analogues. The kinetic studies reveal that the templating Fm7dG slows polβ catalysis ∼300-fold, suggesting that m7dG in genomic DNA may impede replication by some DNA polymerases. The structural analysis reveals that Fm7dG forms a canonical Watson-Crick base pair with dCTP, but metal ion coordination is suboptimal for catalysis in the polβ-Fm7dG:dCTP complex, which partially explains the slow insertion of dCTP opposite Fm7dG by polβ. In addition, the polβ-Fm7dG:dTTP structure shows open protein conformations and staggered base pair conformations, indicating that N7-methylation of dG does not promote a promutagenic replication. Overall, the first systematic studies on the effect of m7dG on DNA replication reveal that polβ catalysis across m7dG is slow, yet highly accurate.