PDBsum entry 1s0m

Transferase/DNA

PDB id: 1s0m

Contents

Protein chains

341 a.a. *

DNA/RNA

Ligands

BAP ×2

DTP ×2

Metals

_CA ×7

_MG

Waters ×337

* Residue conservation analysis

PDB id:

1s0m

Name:

Transferase/DNA

Title:

Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase

Structure:

5'-d( Gp Gp Gp Gp Gp Ap Ap Gp Gp Ap Tp Tp T)-3'. Chain: c, e. Engineered: yes. 5'-d(p Ap Tp Ap Ap Ap Tp Cp Cp Tp Tp Cp Cp Cp Cp Cp A)-3'. Chain: d, f. Engineered: yes. DNA polymerase iv. Chain: a, b. Synonym: pol iv.

Source:

Synthetic: yes. Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2. Gene: dpo4. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.70Å R-factor: 0.207 R-free: 0.246

Authors:

H.Ling,J.M.Sayer,F.Boudsocq,B.S.Plosky,R.Woodgate,W.Yang

Key ref:

H.Ling et al. (2004). Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase. Proc Natl Acad Sci U S A, 101, 2265-2269. PubMed id: 14982998 DOI: 10.1073/pnas.0308332100

Date:

31-Dec-03 Release date: 30-Mar-04

Protein chains

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-T 13 bases

A-T-A-A-A-T-C-C-T-T-C-C-C-C-C-A 16 bases

G-G-G-G-G-A-A-G-G-A-T-T-T 13 bases

A-T-A-A-A-T-C-C-T-T-C-C-C-C-C-A 16 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: 10.1073/pnas.0308332100

Proc Natl Acad Sci U S A 101:2265-2269 (2004)

PubMed id: 14982998

Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase.

H.Ling, J.M.Sayer, B.S.Plosky, H.Yagi, F.Boudsocq, R.Woodgate, D.M.Jerina, W.Yang.

ABSTRACT

The first occupation-associated cancers to be recognized were the sooty warts (cancers of the scrotum) suffered by chimney sweeps in 18th century England. In the 19th century, high incidences of skin cancers were noted among fuel industry workers. By the early 20th century, malignant skin tumors were produced in laboratory animals by repeatedly painting them with coal tar. The culprit in coal tar that induces cancer was finally isolated in 1933 and determined to be benzo[a]pyrene (BP), a polycyclic aromatic hydrocarbon. A residue of fuel and tobacco combustion and frequently ingested by humans, BP is metabolized in mammals to benzo[a]pyrene diol epoxide (BPDE), which forms covalent DNA adducts and induces tumor growth. In the 70 yr since its isolation, BP has been the most studied carcinogen. Yet, there has been no crystal structure of a BPDE DNA adduct. We report here the crystal structure of a BPDE-adenine adduct base-paired with thymine at a template-primer junction and complexed with the lesion-bypass DNA polymerase Dpo4 and an incoming nucleotide. Two conformations of the BPDE, one intercalated between base pairs and another solvent-exposed in the major groove, are observed. The latter conformation, which can be stabilized by organic solvents that reduce the dielectric constant, seems more favorable for DNA replication by Dpo4. These structures also suggest a mechanism by which mutations are generated during replication of DNA containing BPDE adducts.

Selected figure(s)

Figure 2.
Fig. 2. Crystal structures of BP-1 and BP-2. Dpo4 is represented by a purple molecular surface, the DNA and the incoming dATP are shown as blue sticks, and the PAH is highlighted in yellow. The divalent cations (Ca^2+) are shown as green spheres. The unpaired dAMP at the 3' end of the template strand was added by the terminal deoxynucleotide transferase (TdT) activity of Dpo4 that is common to archael D in B-like polymerases (34) (Fig. 4, which is published as supporting information on the PNAS web site). Figs. 2 and 3 were generated by using RIBBONS and GRASP (35, 36).

Figure 3.
Fig. 3. Distortion of DNA by the BPDE adduct. (A) Comparison of the crystal and NMR structures. The dA*·dT and the surrounding base pairs including the replicating base pair are shown as ball-and-stick models. The crystal structures are shown with the F[o] - F[c] omit electron density maps contoured at 1.0 in blue. The carbon, oxygen, nitrogen, and phosphorus atoms are colored yellow, red, blue, and purple, respectively. (B) Hydrogen bond formation at dA*·dT and the adjacent replicating base pair dT·dATP. Looking down the DNA helical axis, the two layers of the base pair and the PAH adduct are shown, purple for the replicating base pair, gold for the dA* adduct, and green for its partner dT. The incoming nucleotide in BP-1 is in the syn conformation. In the BP-2 complex, where the PAH is in the major groove, the adenine base of the dA* is shifted to the major groove, disrupting the normal hydrogen bonds with its partner, dT. The location of a normal dA is modeled in gray. (C) Stereo view of the overlay of the DNA structures from BP-1 (blue) and BP-2 (gold) after superimposition of the Dpo4 structures. With the PAH intercalated, the base pair ladder in the BP-1 complex is shifted by one register compared with that in the BP-2 complex.

Figures were selected by an automated process.