PDBsum entry 5vs4

Transferase, lyase/DNA

PDB id: 5vs4

Contents

Protein chain

327 a.a.

DNA/RNA

Ligands

PPV

ACT ×3

Metals

_MG ×6

Waters ×340

PDB id:

5vs4

Name:

Transferase, lyase/DNA

Title:

Human DNA polymerase beta 8-oxog:da extension with dttp after 120 s

Structure:

DNA (5'-d( Cp Cp Gp Ap Cp Ap (8Og) p Gp Cp Gp Cp Ap Tp Cp Ap G)-3'). Chain: t. Engineered: yes. DNA (5'-d( Cp Tp Gp Ap Tp Gp Cp Gp Cp Ap T)-3'). Chain: p. Engineered: yes. DNA (5'-d(p Gp Tp Cp Gp G)-3'). Chain: d.

Source:

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

Resolution:

1.87Å R-factor: 0.202 R-free: 0.257

Authors:

A.J.Reed,Z.Suo

Key ref:

A.J.Reed and Z.Suo (2017). Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta. J Am Chem Soc, 139, 9684-9690. PubMed id: 28682600 DOI: 10.1021/jacs.7b05048

Date:

11-May-17 Release date: 19-Jul-17

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-A-8OG-G-C-G-C-A-T-C-A-G 16 bases

C-T-G-A-T-G-C-G-C-A-T 11 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

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PPV) corresponds exactly) + 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.7b05048

J Am Chem Soc 139:9684-9690 (2017)

PubMed id: 28682600

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.

A.J.Reed, Z.Suo.

ABSTRACT

The oxidative DNA lesion 7,8-dihydro-2'-deoxyguanine (8-oxoG) often occurs in double-stranded DNA and poses a threat to genomic integrity due to the ability of 8-oxoG to form stable Watson-Crick base pairs with deoxycytidine (8-oxoG:dC) and Hoogsteen base pairs with deoxyadenosine (8-oxoG:dA). In humans, short-patch base excision repair of 8-oxoG:dA base pairs requires human DNA polymerase β (hPolβ) to bypass 8-oxoG. Previously, we have shown hPolβ-catalyzed 8-oxoG bypass to exhibit low fidelity and identified a unique stacking interaction between the newly incorporated nucleotide (dCMP or dAMP) and the templating 8-oxoG. The effect of this stacking on the ability of hPolβ to extend from 8-oxoG during long-patch base excision repair was unknown. Here we report pre-steady-state kinetics and time-dependent crystal structures to demonstrate that extension from both 8-oxoG:dC and 8-oxoG:dA base pairs is 18- to 580-fold less efficient compared to 8-oxoG bypass and that extension from 8-oxoG:dC over 8-oxoG:dA is favored by 15-fold. The overall decrease in efficiency of extension relative to 8-oxoG bypass is due to an alternative nucleotide binding conformation in the precatalytic ternary structures (hPolβ·DNA·dNTP) for both extension contexts, wherein the incoming nucleotide is bound in either the canonical Watson-Crick base pair or a nonplanar base pair. In addition, the decreased stability of the ternary complex of 8-oxoG:dA extension results in further loss of efficiency when compared to 8-oxoG:dC extension. Therefore, we hypothesize that the inefficient extension from 8-oxoG:dA serves as a newly discovered fidelity checkpoint during base excision repair.