PDBsum entry: 1nne

DNA binding protein/DNA

PDB id: 1nne

Contents

Protein chains

759 a.a. *

DNA/RNA

Ligands

SO4 ×2

BEF-ADP ×2

EDO

Waters ×99

* Residue conservation analysis

PDB id:

1nne

Name:

DNA binding protein/DNA

Title:

Crystal structure of the muts-adpbef3-DNA complex

Structure:

5'- d( Gp Cp Gp Ap Cp Gp Cp Tp Ap Gp Cp Gp Tp Gp Cp Gp Gp Cp Tp Cp Gp Tp C)-3'. Chain: c. Engineered: yes. 5'- d(p Gp Gp Ap Cp Gp Ap Gp Cp Cp Gp Cp Cp Gp Cp Tp Ap Gp Cp G p Tp Cp G)-3'. Chain: d.

Source:

Synthetic: yes. Thermus aquaticus. Organism_taxid: 271

Biol. unit:

Tetramer (from PQS)

Resolution:

3.11Å R-factor: 0.209 R-free: 0.259

Authors:

E.Alani,J.Y.Lee,M.J.Schofield,A.W.Kijas,P.Hsieh,W.Yang

Key ref:

E.Alani et al. (2003). Crystal structure and biochemical analysis of the MutS.ADP.beryllium fluoride complex suggests a conserved mechanism for ATP interactions in mismatch repair. J Biol Chem, 278, 16088-16094. PubMed id: 12582174 DOI: 10.1074/jbc.M213193200

Date:

13-Jan-03 Release date: 20-May-03

Protein chains

Q56215  (MUTS_THEAQ) -  DNA mismatch repair protein mutS

Seq: 811 a.a.

Struc: 759 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: response to DNA damage stimulus (3 terms)
• Biochemical function: nucleotide binding (4 terms)

DOI no: 10.1074/jbc.M213193200

J Biol Chem 278:16088-16094 (2003)

PubMed id: 12582174

Crystal structure and biochemical analysis of the MutS.ADP.beryllium fluoride complex suggests a conserved mechanism for ATP interactions in mismatch repair.

E.Alani, J.Y.Lee, M.J.Schofield, A.W.Kijas, P.Hsieh, W.Yang.

ABSTRACT

During mismatch repair ATP binding and hydrolysis activities by the MutS family proteins are important for both mismatch recognition and for transducing mismatch recognition signals to downstream repair factors. Despite intensive efforts, a MutS.ATP.DNA complex has eluded crystallographic analysis. Searching for ATP analogs that strongly bound to Thermus aquaticus (Taq) MutS, we found that ADP.beryllium fluoride (ABF), acted as a strong inhibitor of several MutS family ATPases. Furthermore, ABF promoted the formation of a ternary complex containing the Saccharomyces cerevisiae MSH2.MSH6 and MLH1.PMS1 proteins bound to mismatch DNA but did not promote dissociation of MSH2.MSH6 from mismatch DNA. Crystallographic analysis of the Taq MutS.DNA.ABF complex indicated that although this complex was very similar to that of MutS.DNA.ADP, both ADP.Mg(2+) moieties in the MutS. DNA.ADP structure were replaced by ABF. Furthermore, a disordered region near the ATP-binding pocket in the MutS B subunit became traceable, whereas the equivalent region in the A subunit that interacts with the mismatched nucleotide remained disordered. Finally, the DNA binding domains of MutS together with the mismatched DNA were shifted upon binding of ABF. We hypothesize that the presence of ABF is communicated between the two MutS subunits through the contact between the ordered loop and Domain III in addition to the intra-subunit helical lever arm that links the ATPase and DNA binding domains.

Selected figure(s)

Figure 1.
Fig. 1. The effect of ATP analogs on the Taq MutS, E. coli MutS, and S. cerevisiae MSH2·MSH6 ATPase activities. A, inhibition of Taq MutS ATPase by ATP analogs. Taq MutS and [ -32P]ATP were included at 2.0 and 250 µM, respectively, and ADP (250 µM), tungstate (0.5 mM), vanadate (0.5 mM), BeCl[2] (0.5 mM), AlCl[3] (0.5 mM), and NaF (2.5 mM) were included as indicated. B, ATPase assays performed with 0.5 µM Taq MutS and the indicated concentrations of [ -32P]ATP, ADP, and ABF. C, inhibition of the E. coli MutS ATPase activity by ADP and ABF in the presence and absence of mismatched DNA. ATPase assays performed with 1.0 µM E. coli MutS and ADP, ABF (80 µM), and 35GT mismatch substrate (2.0 µM) were included as indicated. D, inhibition of the MSH2·MSH6 ATPase by ABF. 0.4 µM MSH2·MSH6 was incubated with the indicated concentrations of [ -32P]ATP. ADP (80 µM) and ABF (80 µM) were included in the reactions as indicated. E, inhibition of the MSH2·MSH6 ATPase activity by ABF in the presence and absence of mismatched DNA. 0.1 µM MSH2·MSH6 incubated with 50 µM [ -32P]ATP. ADP (80 or 250 µM), ABF (80 or 250 µM), and 1.0 µM 37-+1 substrate were included in the ATPase reactions as indicated.

Figure 3.
Fig. 3. Crystal structure of a MutS·DNA·ABF complex. A and B, the ABF bound to the A and B subunits shown with the 2(F[o] F[c]) electron density map contoured at 1.0 . The newly formed loop in the B subunit (629-634) shown in green (including 628-638 amino acids) is close to the ABF bound to the A subunit as indicated. C, ribbon diagram of the MutS·DNA·ABF complex. The A subunit is shown in blue, the B subunit in green, DNA duplex in orange, and the loop 629-634 formed in the B subunit is in red. The two ABF and SO[4] ions are shown as ball-and-stick in yellow and pink, respectively. The 629-634 loop of the B subunit is in close contact with residue Arg-267 (shown as light blue ball-and-stick) in the A subunit. Arg-267 is located on a variable loop between residues 263 and 271, which may play a role in communicating between subunits. In addition, DNA associated with MutS·ABF is shifted toward the exit of the DNA-binding channel relative to the DNA associated with MutS·ADP.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 16088-16094) copyright 2003.

Figures were selected by the author.