PDBsum entry 6ph6

Transcription/DNA

PDB id: 6ph6

Contents

Protein chain

326 a.a.

DNA/RNA

Ligands

DCP

Metals

_NA ×2

_MG ×2

Waters ×73

PDB id:

6ph6

Name:

Transcription/DNA

Title:

Ternary complex crystal structure of DNA polymerase beta with 2nt-gap with dctp bound downstream

Structure:

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

Source:

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

Resolution:

2.60Å R-factor: 0.194 R-free: 0.276

Authors:

V.K.Batra,S.H.Wilson

Key ref:

M.J.Howard et al. (2020). DNA polymerase β nucleotide-stabilized template misalignment fidelity depends on local sequence context. J Biol Chem, 295, 529-538. PubMed id: 31801827 DOI: 10.1074/jbc.RA119.010594

Date:

25-Jun-19 Release date: 11-Dec-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-G-G-C-G-C-A-T-C-A-G-C 16 bases

G-C-T-G-A-T-G-C-G 9 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: 10.1074/jbc.RA119.010594

J Biol Chem 295:529-538 (2020)

PubMed id: 31801827

DNA polymerase β nucleotide-stabilized template misalignment fidelity depends on local sequence context.

M.J.Howard, N.A.Cavanaugh, V.K.Batra, D.D.Shock, W.A.Beard, S.H.Wilson.

ABSTRACT

DNA polymerase β has two DNA-binding domains that interact with the opposite sides of short DNA gaps. These domains contribute two activities that modify the 5' and 3' margins of gapped DNA during base excision repair. DNA gaps greater than 1 nucleotide (nt) pose an architectural and logistical problem for the two domains to interact with their respective DNA termini. Here, crystallographic and kinetic analyses of 2-nt gap-filling DNA synthesis revealed that the fidelity of DNA synthesis depends on local sequence context. This was due to template dynamics that altered which of the two template nucleotides in the gap served as the coding nucleotide. We observed that, when a purine nucleotide was in the first coding position, DNA synthesis fidelity was similar to that observed with a 1-nt gap. However, when the initial templating nucleotide was a pyrimidine, fidelity was decreased. If the first templating nucleotide was a cytidine, there was a significantly higher probability that the downstream template nucleotide coded for the incoming nucleotide. This dNTP-stabilized misalignment reduced base substitution and frameshift deletion fidelities. A crystal structure of a binary DNA product complex revealed that the cytidine in the first templating site was in an extrahelical position, permitting the downstream template nucleotide to occupy the coding position. These results indicate that DNA polymerase β can induce a strain in the DNA that modulates the position of the coding nucleotide and thereby impacts the identity of the incoming nucleotide. Our findings demonstrate that "correct" DNA synthesis can result in errors when template dynamics induce coding ambiguity.