PDBsum entry 1s10

Transferase/DNA

PDB id: 1s10

Contents

Protein chain

341 a.a. *

DNA/RNA

Ligands

DCP

Metals

_CA ×2

Waters ×333

* Residue conservation analysis

PDB id:

1s10

Name:

Transferase/DNA

Title:

Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift

Structure:

5'-d( Gp Gp Gp Gp Gp Ap Ap Gp Gp Ap Cp Tp A)-3'. Chain: b. Engineered: yes. 5'-d( Tp Cp Ap Gp Tp Ap Gp Tp Cp Cp Tp Tp Cp Cp Cp Cp C)- 3'. Chain: c. Engineered: yes. DNA polymerase iv. Chain: a.

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:

2.10Å R-factor: 0.216 R-free: 0.239

Authors:

H.Ling,F.Boudsocq,R.Woodgate,W.Yang

Key ref:

H.Ling et al. (2004). Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts. Mol Cell, 13, 751-762. PubMed id: 15023344 DOI: 10.1016/S1097-2765(04)00101-7

Date:

05-Jan-04 Release date: 30-Mar-04

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-C-T-A 13 bases

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

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

Added reference

DOI no: 10.1016/S1097-2765(04)00101-7

Mol Cell 13:751-762 (2004)

PubMed id: 15023344

Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.

H.Ling, F.Boudsocq, R.Woodgate, W.Yang.

ABSTRACT

Dpo4 from S. Solfataricus, a DinB-like Y family polymerase, efficiently replicates DNA past an abasic lesion. We have determined crystal structures of Dpo4 complexed with five different abasic site-containing DNA substrates and find that translesion synthesis is template directed with the abasic site looped out and the incoming nucleotide is opposite the base 5' to the lesion. The ensuing DNA synthesis generates a -1 frameshift when the abasic site remains extrahelical. Template realignment during primer extension is also observed, resulting in base substitutions or even +1 frameshifts. In the case of a +1 frameshift, the extra nucleotide is accommodated in the solvent-exposed minor groove. In addition, the structure of an unproductive Dpo4 ternary complex suggests that the flexible little finger domain facilitates DNA orientation and translocation during translesion synthesis.

Selected figure(s)

Figure 2.
Figure 2. Close-Up Views of the Abasic Lesion in the Ab-1 (A), Ab-2A (B), and Ab-3 (C) ComplexesThese structures represent the likely events when Dpo4 encounters an abasic lesion. Three base pairs including the incoming nucleotide and two metal ions are shown as ball-and-stick models and superimposed with a final refined 2F[o] − F[c] electron density map contoured at 1.0 σ (gray). The template strand is shown in yellow with the abasic site highlighted in green, the primer strand in pink, the incoming nucleotide in purple, and the divalent cations in orange.

Figure 6.
Figure 6. An Extrahelical Base in the Minor Groove(A and B) The inserted base (in dark blue) in the type Ab-4B complex is stacked with the template strand (in red and pink).(C and D) The inserted base in the Ab-5 complex is sandwiched between the primer and template strands. Hydrogen bonds, which stabilize the extrahelical base, are shown in (B) and (D).

The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 13, 751-762) copyright 2004.

Figures were selected by an automated process.