PDBsum entry 6btf

Transferase,lyase/DNA

PDB id: 6btf

Contents

Protein chain

317 a.a.

DNA/RNA

Ligands

DUP

Metals

_NA ×3

_MG

Waters ×337

PDB id:

6btf

Name:

Transferase,lyase/DNA

Title:

DNA polymerase beta i260q ternary complex

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. Mutation: yes. DNA template strand. Chain: t. Engineered: yes. DNA primer strand. 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:

1.75Å R-factor: 0.179 R-free: 0.214

Authors:

B.E.Eckenroth,S.Doublie

Key ref:

C.Liptak et al. (2018). I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity. Nucleic Acids Res, 46, 10740-10756. PubMed id: 30239932 DOI: 10.1093/nar/gky825

Date:

06-Dec-17 Release date: 26-Sep-18

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 317 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

G-A-C-A-G-C-G-C-A-T-C-A-G-C 14 bases

G-C-T-G-A-T-G-C-G-C 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/gky825

Nucleic Acids Res 46:10740-10756 (2018)

PubMed id: 30239932

I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity.

C.Liptak, M.M.Mahmoud, B.E.Eckenroth, M.V.Moreno, K.East, K.S.Alnajjar, J.Huang, J.B.Towle-Weicksel, S.Doublié, J.P.Loria, J.B.Sweasy.

ABSTRACT

DNA polymerase β (pol β) fills single nucleotide gaps in DNA during base excision repair and non-homologous end-joining. Pol β must select the correct nucleotide from among a pool of four nucleotides with similar structures and properties in order to maintain genomic stability during DNA repair. Here, we use a combination of X-ray crystallography, fluorescence resonance energy transfer and nuclear magnetic resonance to show that pol β's ability to access the appropriate conformations both before and upon binding to nucleotide substrates is integral to its fidelity. Importantly, we also demonstrate that the inability of the I260Q mutator variant of pol β to properly navigate this conformational landscape results in error-prone DNA synthesis. Our work reveals that precatalytic conformational rearrangements themselves are an important underlying mechanism of substrate selection by DNA pol β.