PDBsum entry 1xc9

Transferase/DNA

PDB id: 1xc9

Contents

Protein chain

580 a.a. *

DNA/RNA

Ligands

GLC-FRU

BAP

SO4 ×4

Metals

_MG

Waters ×373

* Residue conservation analysis

PDB id:

1xc9

Name:

Transferase/DNA

Title:

Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication

Structure:

DNA primer strand. Chain: b. Engineered: yes. DNA template strand with benzo[a]pyrene adduct. Chain: c. Engineered: yes. Other_details: see remark 400. DNA polymerase i. Chain: a.

Source:

Synthetic: yes. Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

1.90Å R-factor: 0.221 R-free: 0.255

Authors:

G.W.Hsu,X.Huang,N.P.Luneva,N.E.Geacintov,L.S.Beese

Key ref:

G.W.Hsu et al. (2005). Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication. J Biol Chem, 280, 3764-3770. PubMed id: 15548515 DOI: 10.1074/jbc.M411276200

Date:

01-Sep-04 Release date: 14-Dec-04

Protein chain

P52026  (DPO1_GEOSE) -  DNA polymerase I from Geobacillus stearothermophilus

Seq: 876 a.a.

Struc: 580 a.a.*

* PDB and UniProt seqs differ at 67 residue positions (black crosses)

DNA/RNA chains

G-G-G-A-T-G-G-T-G-C 10 bases

C-G-C-A-C-C-A-T-C-C-C-T 12 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

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

Added reference

DOI no: 10.1074/jbc.M411276200

J Biol Chem 280:3764-3770 (2005)

PubMed id: 15548515

Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication.

G.W.Hsu, X.Huang, N.P.Luneva, N.E.Geacintov, L.S.Beese.

ABSTRACT

Of the carcinogens to which humans are most frequently exposed, the polycyclic aromatic hydrocarbon benzo[a]pyrene (BP) is one of the most ubiquitous. BP is a byproduct of grilled foods and tobacco and fuel combustion and has long been linked to various human cancers, particularly lung and skin. BP is metabolized to diol epoxides that covalently modify DNA bases to form bulky adducts that block DNA synthesis by replicative or high fidelity DNA polymerases. Here we present the structure of a high fidelity polymerase from a thermostable strain of Bacillus stearothermophilus (Bacillus fragment) bound to the most common BP-derived N2-guanine adduct base-paired with cytosine. The BP adduct adopts a conformation that places the polycyclic BP moiety in the nascent DNA minor groove and is the first structure of a minor groove adduct bound to a polymerase. Orientation of the BP moiety into the nascent DNA minor groove results in extensive disruption to the interactions between the adducted DNA duplex and the polymerase. The disruptions revealed by the structure of Bacillus fragment bound to a BP adduct provide a molecular basis for rationalizing the potent blocking effect on replication exerted by BP adducts.

Selected figure(s)

Figure 2.
FIG. 2. [BP]dG at the post-insertion site of the BF active site. Stereoview of the structure of BF bound to BP-modified DNA duplex (red) superimposed on the structure of BF bound to unmodified DNA duplex (gray). A schematic representing the BF active site is shown below.

Figure 3.
FIG. 3. [BP]dG-induced distortions to the BF polymerase active site. A, the C:[BP]dG base pair surrounded by omit electron density contoured at 3 with hydrogen bonds represented in black (dashed lines) accompanied by lengths. B, superposition of the BP-modified DNA duplex (red) and an unmodified DNA duplex (gray). The BP moiety of the [BP]dG protrudes into the DNA minor groove. C, comparison of BF protein side chain conformations when BF is bound to C:[BP]dG (red) and C:G (gray) at the post-insertion site (n-1 position). Hydrogen bonds are represented as dashed lines. D, model of BF in a ternary complex with [BP]dG (yellow) obstructing the insertion site to an incoming dCTP. A cognate base pair is shown in gray, and hydrogen bonds are represented by dashed lines.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 3764-3770) copyright 2005.

Figures were selected by an automated process.