PDBsum entry: 1ng9

DNA binding protein

PDB id: 1ng9

Contents

Protein chains

794 a.a. *

DNA/RNA

Ligands

ADP ×2

Metals

_MG ×2

Waters ×364

* Residue conservation analysis

PDB id:

1ng9

Name:

DNA binding protein

Title:

E.Coli muts r697a: an atpase-asymmetry mutant

Structure:

5'-d( Ap Gp Cp Tp Gp Cp Cp Ap Gp Gp Cp Ap Cp Cp A Tp Cp Ap Gp Cp Gp Tp Cp Cp Tp Ap T)-3'. Chain: e. Engineered: yes. 5'-d( Ap Tp Ap Gp Gp Ap Cp Gp Cp Tp Gp Ap Cp Ap C Tp Gp Cp Tp Tp Gp Gp Cp Ap Gp Cp T)-3'. Chain: f. Engineered: yes. DNA mismatch repair protein muts.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: muts. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.60Å R-factor: 0.216 R-free: 0.249

Authors:

M.H.Lamers,H.H.K.Winterwerp,T.K.Sixma

Key ref:

M.H.Lamers et al. (2003). The alternating ATPase domains of MutS control DNA mismatch repair. EMBO J, 22, 746-756. PubMed id: 12554674 DOI: 10.1093/emboj/cdg064

Date:

17-Dec-02 Release date: 11-Feb-03

Protein chains

P23909  (MUTS_ECOLI) -  DNA mismatch repair protein mutS

Seq: 853 a.a.

Struc: 794 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Biological process: response to DNA damage stimulus (4 terms)
• Biochemical function: nucleotide binding (9 terms)

DOI no: 10.1093/emboj/cdg064

EMBO J 22:746-756 (2003)

PubMed id: 12554674

The alternating ATPase domains of MutS control DNA mismatch repair.

M.H.Lamers, H.H.Winterwerp, T.K.Sixma.

ABSTRACT

DNA mismatch repair is an essential safeguard of genomic integrity by removing base mispairings that may arise from DNA polymerase errors or from homologous recombination between DNA strands. In Escherichia coli, the MutS enzyme recognizes mismatches and initiates repair. MutS has an intrinsic ATPase activity crucial for its function, but which is poorly understood. We show here that within the MutS homodimer, the two chemically identical ATPase sites have different affinities for ADP, and the two sites alternate in ATP hydrolysis. A single residue, Arg697, located at the interface of the two ATPase domains, controls the asymmetry. When mutated, the asymmetry is lost and mismatch repair in vivo is impaired. We propose that asymmetry of the ATPase domains is an essential feature of mismatch repair that controls the timing of the different steps in the repair cascade.

Selected figure(s)

Figure 3.
Figure 3 Vanadate trapping and ATPase inhibition. (A) MutS (5 M) was incubated with radiolabelled ATP with or without vanadate (V[i]). Samples were spotted directly onto nitrocellulose filters or washed first with a large excess of unlabelled ATP as indicated. (B and C) ATPase inhibition in wild-type and R697A MutS. In conditions identical to (A), MutS was incubated with unlabelled ATP with or without vanadate, after which labelled ATP was added to measure ATPase activity.

Figure 6.
Figure 6 Structural analysis of asymmetry. (A) Structure of the MutS dimer in complex with mismatched DNA. Protein is coloured in grey, with ATPase domains of monomer A and B coloured in green and blue, respectively, and mismatch binding domains of monomer A and B in light green and light blue. DNA and ADP are in red. (B) The two ATPase domains viewed along the arrow in (A). The ADP molecule in monomer A is coloured in brown; the side chains of the two Arg697 (coloured in grey) are located at the centre of the interface of the two ATPase domains. (C) Schematic representation of the asymmetric interactions of the ATPase domains of monomer A (green) and B (blue). (1) ArgB697 hydrogen-bonds to the backbone of GlyA698 in the DE-loop of monomer A, while the reverse contact does not take place. (2) As a result, the DE-loop of monomer A clashes with the P-loop of monomer B, which is thus inhibited from nucleotide binding. (3) Simultaneously, ArgB697 also hydrogen-bonds to and displaces GluB694. (D) Close-up of the nucleotide-binding site of monomer A in green, with the opposing monomer B in blue. (E) Same view as (D), but now viewed from monomer B. (F) Same view as (E), but of R697A MutS. The position of the DE-loop in monomer A and B of wild-type MutS is indicated in grey and black, respectively. In the absence of Arg697, no contacts are made between the two DE-loops, and both monomer A and B now bind ADP-Mg2+. (G) Structure-based sequence alignment of MutS homologues and paralogues, and related ATPases. The conserved Arg697 is coloured in orange, and marked with an asterisk (*). The Walker B motif is boxed, and indicated by (**). Secondary structural elements are indicated by a green arrow ( -strand) or a blue tube ( -helix). PDB accession codes E.coli MutS, 1E3M; Taq MutS, 1EWQ; RAD50, 1F2U; SMC, 1E69; TAP1, 1JJ7; HisP, 1B0U; MalK, 1G29; RecA, 2REB; RepA, 1G8Y; gp4, 1E0J; F1, 1BMF.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 746-756) copyright 2003.

Figures were selected by the author.