PDBsum entry: 1e3m

DNA binding

PDB id: 1e3m

Contents

Protein chains

788 a.a. *

DNA/RNA

Ligands

ADP

Metals

_MG ×2

Waters ×478

* Residue conservation analysis

PDB id:

1e3m

Name:

DNA binding

Title:

The crystal structure of e. Coli muts binding to DNA with a g:t mismatch

Structure:

DNA mismatch repair protein muts. Chain: a, b. Fragment: residues 1-800. Engineered: yes. 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 T)-3'. Chain: e. Other_details: g\:t mismatch DNA. 5'-d( Ap Tp Ap Gp Gp Ap Cp Gp Cp Tp Gp Ap Cp Ap Cp

Source:

Escherichia coli. Organism_taxid: 562. Cellular_location: nucleus. Gene: muts. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: plyss. Synthetic: DNA oligonucleotides, annealed. Organism_taxid: 562

Biol. unit:

Dimer (from PDB file)

Resolution:

2.20Å R-factor: 0.229 R-free: 0.266

Authors:

M.H.Lamers,A.Perrakis,J.H.Enzlin,H.H.K.Winterwerp,N.De Wind, T.K.Sixma

Key ref:

M.H.Lamers et al. (2000). The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch. Nature, 407, 711-717. PubMed id: 11048711 DOI: 10.1038/35037523

Date:

19-Jun-00 Release date: 01-Nov-00

Protein chains

P23909  (MUTS_ECOLI) -  DNA mismatch repair protein mutS

Seq: 853 a.a.

Struc: 788 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: mismatch repair complex (1 term)
• Biological process: response to DNA damage stimulus (4 terms)
• Biochemical function: nucleotide binding (9 terms)

DOI no: 10.1038/35037523

Nature 407:711-717 (2000)

PubMed id: 11048711

The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch.

M.H.Lamers, A.Perrakis, J.H.Enzlin, H.H.Winterwerp, N.de Wind, T.K.Sixma.

ABSTRACT

DNA mismatch repair ensures genomic integrity on DNA replication. Recognition of a DNA mismatch by a dimeric MutS protein initiates a cascade of reactions and results in repair of the newly synthesized strand; however, details of the molecular mechanism remain controversial. Here we present the crystal structure at 2.2 A of MutS from Escherichia coli bound to a G x T mismatch. The two MutS monomers have different conformations and form a heterodimer at the structural level. Only one monomer recognizes the mismatch specifically and has ADP bound. Mismatch recognition occurs by extensive minor groove interactions causing unusual base pairing and kinking of the DNA. Nonspecific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. The interleaved nucleotide-binding sites are located far from the DNA. Mutations in human MutS alpha (MSH2/MSH6) that lead to hereditary predisposition for cancer, such as hereditary non-polyposis colorectal cancer, can be mapped to this crystal structure.

Selected figure(s)

Figure 2.
Figure 2: Mismatch-binding monomer coloured by domain. The mismatch-binding domain (2-115) is coloured dark blue, the connector domain (116-266) light blue, the core domain and levers (267-443 + 504-567) from red to orange, the clamp domain (444-503) orange, the ATPase domain (568-765) green, and HTH (766-800) yellow.

Figure 3.
Figure 3: Interaction of MutS with mismatched DNA. a, Overview showing MutS embracing the DNA mismatch-binding domain in dark blue, its lever and clamp domains in red to orange, and lever and clamp domains of the second monomer in light blue. DNA and ADP are coloured red, the rest of the structure is grey. b, Side view, showing all residues involved in hydrogen bonds and salt bridges to DNA. Mismatch is coloured yellow, c, Top view, showing the asymmetric binding of the clamp domains. d, Stereo view of the sigma A-weighted (2mF[o]- DF [c] )43 electron density map contoured at 1.0 r.m.s. displaying stacking of Phe 36 (dark blue) on the mismatched thymine 22 (yellow). e, Diagram of all hydrogen bonds and salt bridges (in italics) made to DNA. Residues are coloured by domain as in a; nonspecific contacts are boxed. Sugar puckering of C3' endo (A form DNA) is indicated by light blue colouring of riboses. f, Mismatch-specific hydrogen bonding. The G T mismatch does not pair as a wobble base, which would have hydrogen bonds between guanine O6 and thymine N3, and guanine N1 and thymine O2. g, Electrostatic surface representation48 of mismatch-recognition domain in contact with DNA (stick model), displaying the lack of positive charge in the interface. Electrostatic charges (red, negative; blue, positive) are shown between -10 and +10 kT. Mismatched bases are labelled, as well as the approximate surface area of Phe 36, Asp 35 and Glu 38.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2000, 407, 711-717) copyright 2000.

Figures were selected by the author.