PDBsum entry 1ua0

Transferase/DNA

PDB id: 1ua0

Contents

Protein chain

580 a.a. *

DNA/RNA

Ligands

GLC-FRU

_AF

SO4 ×2

Waters ×316

* Residue conservation analysis

PDB id:

1ua0

Name:

Transferase/DNA

Title:

Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase

Structure:

DNA primer strand. Chain: b. Engineered: yes. DNA template strand with aminofluorene 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:

2.10Å R-factor: 0.210 R-free: 0.242

Authors:

G.W.Hsu,J.R.Kiefer,O.J.Becherel,R.P.P.Fuchs,L.S.Beese

Key ref:

G.W.Hsu et al. (2004). Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase. J Biol Chem, 279, 50280-50285. PubMed id: 15385534 DOI: 10.1074/jbc.M409224200

Date:

11-Aug-04 Release date: 28-Sep-04

Protein chain

Q5KWC1  (Q5KWC1_GEOKA) -  DNA polymerase I from Geobacillus kaustophilus (strain HTA426)

Seq: 878 a.a.

Struc: 580 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

G-G-G-A-T-G-G-T-G 9 bases

T-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.M409224200

J Biol Chem 279:50280-50285 (2004)

PubMed id: 15385534

Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase.

G.W.Hsu, J.R.Kiefer, D.Burnouf, O.J.Becherel, R.P.Fuchs, L.S.Beese.

ABSTRACT

Aromatic amines have been studied for more than a half-century as model carcinogens representing a class of chemicals that form bulky adducts to the C8 position of guanine in DNA. Among these guanine adducts, the N-(2'-deoxyguanosin-8-yl)-aminofluorene (G-AF) and N-2-(2'-deoxyguanosin-8-yl)-acetylaminofluorene (G-AAF) derivatives are the best studied. Although G-AF and G-AAF differ by only an acetyl group, they exert different effects on DNA replication by replicative and high-fidelity DNA polymerases. Translesion synthesis of G-AF is achieved with high-fidelity polymerases, whereas replication of G-AAF requires specialized bypass polymerases. Here we have presented structures of G-AF as it undergoes one round of accurate replication by a high-fidelity DNA polymerase. Nucleotide incorporation opposite G-AF is achieved in solution and in the crystal, revealing how the polymerase accommodates and replicates past G-AF, but not G-AAF. Like an unmodified guanine, G-AF adopts a conformation that allows it to form Watson-Crick hydrogen bonds with an opposing cytosine that results in protrusion of the bulky fluorene moiety into the major groove. Although incorporation opposite G-AF is observed, the C:G-AF base pair induces distortions to the polymerase active site that slow translesion synthesis.

Selected figure(s)

Figure 1.
FIG. 1. A, chemical structures of G-AF and G-AAF. dR, deoxyribose ring. The proton and the N-acetyl group that differentiate G-AF from G-AAF are shown in orange. B, schematic of the polymerase active site. Sites through which the template base (red) traverses during replication are shown (see the Introduction for description).

Figure 4.
FIG. 4. Structure of BF with G-AF at the postinsertion site. A, structure of BF bound to G-AF at the postinsertion site (blue) superimposed with a structure of BF bound to an unmodified base at the postinsertion site (gray). G-AF (red) adopts an anti conformation and obstructs the n+1 template base from occupying the preinsertion site that is itself disordered. B, C:G-AF base pair surrounded by electron density contoured at 3.5 and calculated using Fourier coefficients (F[obs] - F[calc]) [calc] with C:G-AF omitted from the final model. Hydrogen bonds (dashed lines) are shown accompanied with bond lengths.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 50280-50285) copyright 2004.

Figures were selected by an automated process.