PDBsum entry: 1wbb

DNA-binding

PDB id: 1wbb

Contents

Protein chains

788 a.a. *

DNA/RNA

Ligands

ADP

Metals

_MG

Waters ×285

* Residue conservation analysis

PDB id:

1wbb

Name:

DNA-binding

Title:

Crystal structure of e. Coli DNA mismatch repair enzyme muts, e38a mutant, in complex with a g.T mismatch

Structure:

DNA mismatch repair protein muts. Chain: a, b. Fragment: residues 1-800. Engineered: yes. Mutation: yes. 5'-d( Ap Gp Cp Tp Gp Cp Cp Ap Gp Gp Cp Ap Cp Cp Ap Gp Tp G)-3'. Chain: e. Engineered: yes.

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: plyss. Synthetic: yes. Synthetic: yes

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.50Å R-factor: 0.221 R-free: 0.270

Authors:

G.Natrajan,D.Georgijevic,J.H.G.Lebbink,H.H.K.Winterwerp,N.De T.K.Sixma

Key ref:

J.H.Lebbink et al. (2006). Dual role of MutS glutamate 38 in DNA mismatch discrimination and in the authorization of repair. EMBO J, 25, 409-419. PubMed id: 16407973 DOI: 10.1038/sj.emboj.7600936

Date:

31-Oct-04 Release date: 18-Jan-06

Protein chains

P23909  (MUTS_ECOLI) -  DNA mismatch repair protein mutS

Seq: 853 a.a.

Struc: 788 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: 10.1038/sj.emboj.7600936

EMBO J 25:409-419 (2006)

PubMed id: 16407973

Dual role of MutS glutamate 38 in DNA mismatch discrimination and in the authorization of repair.

J.H.Lebbink, D.Georgijevic, G.Natrajan, A.Fish, H.H.Winterwerp, T.K.Sixma, N.de Wind.

ABSTRACT

MutS plays a critical role in DNA mismatch repair in Escherichia coli by binding to mismatches and initiating repair in an ATP-dependent manner. Mutational analysis of a highly conserved glutamate, Glu38, has revealed its role in mismatch recognition by enabling MutS to discriminate between homoduplex and mismatched DNA. Crystal structures of MutS have shown that Glu38 forms a hydrogen bond to one of the mismatched bases. In this study, we have analyzed the crystal structures, DNA binding and the response to ATP binding of three Glu38 mutants. While confirming the role of the negative charge in initial discrimination, we show that in vivo mismatch repair can proceed even when discrimination is low. We demonstrate that the formation of a hydrogen bond by residue 38 to the mismatched base authorizes repair by inducing intramolecular signaling, which results in the inhibition of rapid hydrolysis of distally bound ATP. This allows formation of the stable MutS-ATP-DNA clamp, a key intermediate in triggering downstream repair events.

Selected figure(s)

Figure 1.
Figure 1 Crystal structures of wild-type MutS and E38 variants. (A) Schematic view of the E. coli MutS dimer, with the mismatch-binding monomer A shown in yellow, the supporting monomer B shown in orange and the mismatch containing DNA in blue. (B) Superposition of the mismatch-binding clamp domains and DNA of wild-type and mutant MutS obtained by superposing the C atoms of the mismatch-binding monomer A of all the structures. (C) G.T mismatch binding by the wild-type MutS. (D) G.T mismatch binding by the E38T mutant, with the bound water molecule in red, along with its mF[o]-DF[c] map contoured at 3 (in green). (E) G.T mismatch binding by the E38Q mutant. (F) G.T mismatch binding by E38A, shown with the bound water molecule (in red) along with its mF[o]-DF[c] density map contoured at 3 (in green). Dashed red lines indicate hydrogen bonds and residue 38 in panels C-F is shown in purple. All figures were made using PyMOL (Copyright© 2004 DeLano Scientific).

Figure 5.
Figure 5 Kinetic response to ATP binding of wild-type MutS and E38 mutants. (A) Magnitude of burst amplitude of ADP formation during the first hydrolytic turnover in a rapid quench ATPase assay in the absence and presence of DNA containing a G.T mismatch. (B) Kinetics of ATP-induced MutS release from mismatched (mm) DNA with a free end and (C) from double end-blocked mismatched DNA determined by SPR.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 409-419) copyright 2006.

Figures were selected by the author.