PDBsum entry: 1w7a

DNA binding

PDB id: 1w7a

Contents

Protein chains

791 a.a. *

DNA/RNA

Ligands

ATP ×2

Metals

_MG

Waters ×266

* Residue conservation analysis

PDB id:

1w7a

Name:

DNA binding

Title:

Atp bound muts

Structure:

DNA mismatch repair protein muts. Chain: a, b. Fragment: residues 1-800. Engineered: yes. Other_details: DNA oligomer containing gt mismatch adenosin triphosphate (atp). 5'-d( Ap Gp Cp Tp Gp Cp Cp Ap Gp Gp Cp Ap Cp Cp Ap Gp Tp Gp Tp Cp Ap Gp Cp Gp Tp Cp Cp Tp Ap chain: e.

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.27Å R-factor: 0.217 R-free: 0.253

Authors:

M.H.Lamers,D.Georgijevic,J.Lebbink,H.H.K.Winterwerp,B.Agiani N.De Wind,T.K.Sixma

Key ref:

M.H.Lamers et al. (2004). ATP increases the affinity between MutS ATPase domains. Implications for ATP hydrolysis and conformational changes. J Biol Chem, 279, 43879-43885. PubMed id: 15297450 DOI: 10.1074/jbc.M406380200

Date:

31-Aug-04 Release date: 10-Sep-04

Protein chains

P23909  (MUTS_ECOLI) -  DNA mismatch repair protein mutS

Seq: 853 a.a.

Struc: 791 a.a.

 Gene Ontology (GO) functional annotation 

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

DOI no: 10.1074/jbc.M406380200

J Biol Chem 279:43879-43885 (2004)

PubMed id: 15297450

ATP increases the affinity between MutS ATPase domains. Implications for ATP hydrolysis and conformational changes.

M.H.Lamers, D.Georgijevic, J.H.Lebbink, H.H.Winterwerp, B.Agianian, N.de Wind, T.K.Sixma.

ABSTRACT

MutS is the key protein of the Escherichia coli DNA mismatch repair system. It recognizes mispaired and unpaired bases and has intrinsic ATPase activity. ATP binding after mismatch recognition by MutS serves as a switch that enables MutL binding and the subsequent initiation of mismatch repair. However, the mechanism of this switch is poorly understood. We have investigated the effects of ATP binding on the MutS structure. Crystallographic studies of ATP-soaked crystals of MutS show a trapped intermediate, with ATP in the nucleotide-binding site. Local rearrangements of several residues around the nucleotide-binding site suggest a movement of the two ATPase domains of the MutS dimer toward each other. Analytical ultracentrifugation experiments confirm such a rearrangement, showing increased affinity between the ATPase domains upon ATP binding and decreased affinity in the presence of ADP. Mutations of specific residues in the nucleotide-binding domain reduce the dimer affinity of the ATPase domains. In addition, ATP-induced release of DNA is strongly reduced in these mutants, suggesting that the two activities are coupled. Hence, it seems plausible that modulation of the affinity between ATPase domains is the driving force for conformational changes in the MutS dimer. These changes are driven by distinct amino acids in the nucleotide-binding site and form the basis for long-range interactions between the ATPase domains and DNA-binding domains and subsequent binding of MutL and initiation of mismatch repair.

Selected figure(s)

Figure 1.
FIG. 1. Structure of MutS in complex with DNA and ATP. A, overview of the complex with ATPase domains of monomer A and B colored green and blue, respectively. Electron density covering the ATP molecules is colored dark blue. Signature loops are in red, and missing residues are transparent. The rest of the molecule is colored gray. DNA is dark red. B, enlarged view of A showing the position of the nucleotides and signature loops. C, overview of the ATPase dimer interface showing only the ATPase domains. D and E, detailed view of the nucleotide-binding site of monomer A binding ADP or ATP, respectively. Monomer A is colored green, and the opposing monomer B is blue, with missing residues transparent. Note the rotation of residues Asn616 and His728 and the stabilization of Ser668 and the larger part of the loop on which it resides. F, nucleotide-binding site of monomer B binding ATP. Asn616, indicated as transparent, is poorly defined in electron density.

Figure 3.
FIG. 3. Modeling of conformational changes induced by ATP binding. A, model of MutS after superposition of the MutS ATPase domains on the ATPase domains of RAD50-ATP (see "Discussion"). In addition to an 5 Å translation, an 25° degrees rotation of the two monomers toward one another is observed. B-D, model for ATP-induced DNA release. In the absence of DNA (B), the DNA-binding domains (clamp and mismatch, indicated by "C" and "M") are flexible and opened up to allow the DNA to enter. When a mismatch is bound (shown in yellow), the DNA is kinked and surrounded by the two monomers (C). Subsequent ATP binding (D) causes a further closing of the clamp. To avoid the clashing of the mismatch binding domains, they are rotated away from the DNA, leaving MutS as a sliding clamp on the DNA.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 43879-43885) copyright 2004.

Figures were selected by the author.