PDBsum entry 4pha

Transferase,lyase/DNA

PDB id: 4pha

Contents

Protein chain

327 a.a.

DNA/RNA

Ligands

0KX

Metals

_MG ×2

_NA ×2

Waters ×74

PDB id:

4pha

Name:

Transferase,lyase/DNA

Title:

Structure of human DNA polymerase beta complexed with a in the template base paired with incoming non-hydrolyzable ctp

Structure:

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

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: enterobacteria phage l1. Expression_system_taxid: 268588. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.52Å R-factor: 0.220 R-free: 0.278

Authors:

M.C.Koag,S.Lee

Key ref:

M.C.Koag et al. (2014). The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β. Nucleic Acids Res, 42, 11233-11245. PubMed id: 25200079 DOI: 10.1093/nar/gku789

Date:

05-May-14 Release date: 24-Sep-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-A-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/gku789

Nucleic Acids Res 42:11233-11245 (2014)

PubMed id: 25200079

The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β.

M.C.Koag, K.Nam, S.Lee.

ABSTRACT

To provide molecular-level insights into the spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β (polβ), we report four crystal structures of polβ complexed with dG•dTTP and dA•dCTP mismatches in the presence of Mg(2+) or Mn(2+). The Mg(2+)-bound ground-state structures show that the dA•dCTP-Mg(2+) complex adopts an 'intermediate' protein conformation while the dG•dTTP-Mg(2+) complex adopts an open protein conformation. The Mn(2+)-bound 'pre-chemistry-state' structures show that the dA•dCTP-Mn(2+) complex is structurally very similar to the dA•dCTP-Mg(2+) complex, whereas the dG•dTTP-Mn(2+) complex undergoes a large-scale conformational change to adopt a Watson-Crick-like dG•dTTP base pair and a closed protein conformation. These structural differences, together with our molecular dynamics simulation studies, suggest that polβ increases replication fidelity via a two-stage mismatch discrimination mechanism, where one is in the ground state and the other in the closed conformation state. In the closed conformation state, polβ appears to allow only a Watson-Crick-like conformation for purine•pyrimidine base pairs, thereby discriminating the mismatched base pairs based on their ability to form the Watson-Crick-like conformation. Overall, the present studies provide new insights into the spontaneous replication error and the replication fidelity mechanisms of polβ.