PDBsum entry 2ibk

Transferase/DNA

PDB id: 2ibk

Contents

Protein chain

341 a.a. *

DNA/RNA

Ligands

BAP

EDO ×3

GOL

POP

Metals

_CA ×2

Waters ×201

* Residue conservation analysis

PDB id:

2ibk

Name:

Transferase/DNA

Title:

Bypass of major benzopyrene-dg adduct by y-family DNA polymerase with unique structural gap

Structure:

5'-d( Gp Gp Gp Gp Gp Ap Ap Gp Gp Ap Tp Tp Ap T)-3'. Chain: d. Engineered: yes. 5'-d( Tp Cp Ap Tp Gp Ap Ap Tp Cp Cp Tp Tp Cp Cp Cp Cp C)- 3'. Chain: e. Engineered: yes. DNA polymerase iv. Chain: a.

Source:

Synthetic: yes. Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2. Gene: dbh, dpo4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.25Å R-factor: 0.250 R-free: 0.272

Authors:

J.Bauer,H.Ling,J.M.Sayer,G.Xing,H.Yagi,D.M.Jerina

Key ref:

J.Bauer et al. (2007). A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment. Proc Natl Acad Sci U S A, 104, 14905-14910. PubMed id: 17848527 DOI: 10.1073/pnas.0700717104

Date:

11-Sep-06 Release date: 11-Sep-07

Protein chain

Q97W02  (DPO4_SULSO) -  DNA polymerase IV from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 352 a.a.

Struc: 341 a.a.

DNA/RNA chains

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

T-C-A-T-G-A-A-T-C-C-T-T-C-C-C-C-C 17 bases

Enzyme reactions

• Enzyme class: 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 = POP) corresponds exactly) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1073/pnas.0700717104

Proc Natl Acad Sci U S A 104:14905-14910 (2007)

PubMed id: 17848527

A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment.

J.Bauer, G.Xing, H.Yagi, J.M.Sayer, D.M.Jerina, H.Ling.

ABSTRACT

Erroneous replication of lesions in DNA by DNA polymerases leads to elevated mutagenesis. To understand the molecular basis of DNA damage-induced mutagenesis, we have determined the x-ray structures of the Y-family polymerase, Dpo4, in complex with a DNA substrate containing a bulky DNA lesion and incoming nucleotides. The DNA lesion is derived from an environmentally widespread carcinogenic polycyclic aromatic hydrocarbon, benzo[a]pyrene (BP). The potent carcinogen BP is metabolized to diol epoxides that form covalent adducts with cellular DNA. In the present study, the major BP diol epoxide adduct in DNA, BP-N(2)-deoxyguanosine (BP-dG), was placed at a template-primer junction. Three ternary complexes reveal replication blockage, extension past a mismatched lesion, and a -1 frameshift mutation. In the productive structures, the bulky adduct is flipped/looped out of the DNA helix into a structural gap between the little finger and core domains. Sequestering of the hydrophobic BP adduct in this new substrate-binding site permits the DNA to exhibit normal geometry for primer extension. Extrusion of the lesion by template misalignment allows the base 5' to the adduct to serve as the template, resulting in a -1 frameshift. Subsequent strand realignment produces a mismatched base opposite the lesion. These structural observations, in combination with replication and mutagenesis data, suggest a model in which the additional substrate-binding site stabilizes the extrahelical nucleotide for lesion bypass and generation of base substitutions and -1 frameshift mutations.

Selected figure(s)

Figure 2.
Structures of BPG-1A, BPG-1B and BPG-2. (A–C) Dpo4 is represented as a molecular surface with the polymerase core in cyan and the LF domain in purple; DNA and nucleotide are shown as sticks, and BP–dG is highlighted in orange. BPG-1B and BPG-2 in B and C are rotated 180° relative to BPG-1A in A around the DNA helix axis, to show the extrahelical BP–dG in the gap between the core and LF domains. (D–F) The DNA conformations corresponding to (A–C) as stick models, all with the same orientations as in A. The primer strands are in gray, and incoming dATP is in pink. The single-stranded portion of the template DNA is not shown. Figs. 2, 3, and 4 were generated by using PYMOL (46).

Figure 4.
Close-up views of BP–dG in the structure gap between the core and the LF domains. (A) BPG-1B. (B) BPG-2. The protein is in ribbon models covered by a transparent molecular surface. The key residues interacting with the adduct G* are shown as stick models. The BP ring system is in van der Waals contact with the LF domain (purple); the adducted G base interacts with the core domain (cyan). The glycerol molecule is in gray.

Figures were selected by an automated process.