PDBsum entry 4rpy

Transferase/DNA

PDB id: 4rpy

Contents

Protein chain

326 a.a.

DNA/RNA

Ligands

ACT ×2

PPV-DCP

DCP

Metals

_NA ×7

_MG ×3

_CL ×4

Waters ×286

PDB id:

4rpy

Name:

Transferase/DNA

Title:

Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8- dihydro-guanine(8-oxog) and dctp soaked with mgcl2 for 30 s

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. DNA (5'-d(p Gp Tp Cp Gp G)-3'). Chain: d. Synonym: 5-mer phosphorylated downstream primer. Engineered: yes. DNA (5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp Cp C)-3'). Chain: p.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pol b, polb. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

1.90Å R-factor: 0.192 R-free: 0.230

Authors:

R.Vyas,Z.Suo

Key ref:

R.Vyas et al. (2015). Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography. J Am Chem Soc, 137, 5225-5230. PubMed id: 25825995 DOI: 10.1021/jacs.5b02109

Date:

31-Oct-14 Release date: 15-Apr-15

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 326 a.a.

DNA/RNA chains

G-T-C-G-G 5 bases

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

C-C-G-A-C-8OG-G-C-G-C-A-T-C-A-G-C 16 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.5b02109

J Am Chem Soc 137:5225-5230 (2015)

PubMed id: 25825995

Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.

R.Vyas, A.J.Reed, E.J.Tokarsky, Z.Suo.

ABSTRACT

One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson-Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg(2+) appeared during the process of phosphodiester bond formation and was located between the reacting α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.