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PDBsum entry 1oh8

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protein dna_rna ligands metals Protein-protein interface(s) links
DNA binding PDB id
1oh8
Jmol
Contents
Protein chains
788 a.a. *
DNA/RNA
Ligands
ADP
Metals
_MG
Waters ×137
* Residue conservation analysis
PDB id:
1oh8
Name: DNA binding
Title: The crystal structure of e. Coli muts binding to DNA with an unpaired thymidine
Structure: DNA mismatch repair protein muts. Chain: a, b. Fragment: residues 1-800. Synonym: muts, fdv, b2733. 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 chain: e. Other_details: DNA with unpaired thymidine-top strand.
Source: Escherichia coli. Organism_taxid: 562. Strain: b834 de3. Variant: plyss. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: plyss. Synthetic: yes. Other_details: chemically synthesized.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.90Å     R-factor:   0.221     R-free:   0.292
Authors: G.Natrajan,M.H.Lamers,J.H.Enzlin,H.H.K.Winterwerp,A.Perrakis T.K.Sixma
Key ref: G.Natrajan et al. (2003). Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates. Nucleic Acids Res, 31, 4814-4821. PubMed id: 12907723 DOI: 10.1093/nar/gkg677
Date:
23-May-03     Release date:   08-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23909  (MUTS_ECOLI) -  DNA mismatch repair protein MutS
Seq:
Struc:
 
Seq:
Struc:
853 a.a.
788 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mismatch repair complex   2 terms 
  Biological process     response to DNA damage stimulus   5 terms 
  Biochemical function     nucleotide binding     11 terms  

 

 
DOI no: 10.1093/nar/gkg677 Nucleic Acids Res 31:4814-4821 (2003)
PubMed id: 12907723  
 
 
Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates.
G.Natrajan, M.H.Lamers, J.H.Enzlin, H.H.Winterwerp, A.Perrakis, T.K.Sixma.
 
  ABSTRACT  
 
We have refined a series of isomorphous crystal structures of the Escherichia coli DNA mismatch repair enzyme MutS in complex with G:T, A:A, C:A and G:G mismatches and also with a single unpaired thymidine. In all these structures, the DNA is kinked by approximately 60 degrees upon protein binding. Two residues widely conserved in the MutS family are involved in mismatch recognition. The phenylalanine, Phe 36, is seen stacking on one of the mismatched bases. The same base is also seen forming a hydrogen bond to the glutamate Glu 38. This hydrogen bond involves the N7 if the base stacking on Phe 36 is a purine and the N3 if it is a pyrimidine (thymine). Thus, MutS uses a common binding mode to recognize a wide range of mismatches.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22179786 S.Gupta, M.Gellert, and W.Yang (2012).
Mechanism of mismatch recognition revealed by human MutSĪ² bound to unpaired DNA loops.
  Nat Struct Mol Biol, 19, 72-78.
PDB codes: 3thw 3thx 3thy 3thz
20167596 J.H.Lebbink, A.Fish, A.Reumer, G.Natrajan, H.H.Winterwerp, and T.K.Sixma (2010).
Magnesium coordination controls the molecular switch function of DNA mismatch repair protein MutS.
  J Biol Chem, 285, 13131-13141.
PDB codes: 2wtu 3k0s
20421420 J.M.Dowen, C.D.Putnam, and R.D.Kolodner (2010).
Functional studies and homology modeling of Msh2-Msh3 predict that mispair recognition involves DNA bending and strand separation.
  Mol Cell Biol, 30, 3321-3328.  
  20725617 K.Fukui (2010).
DNA mismatch repair in eukaryotes and bacteria.
  J Nucleic Acids, 2010, 0.  
20180598 L.E.Sass, C.Lanyi, K.Weninger, and D.A.Erie (2010).
Single-molecule FRET TACKLE reveals highly dynamic mismatched DNA-MutS complexes.
  Biochemistry, 49, 3174-3190.  
20097818 M.C.Turrientes, M.R.Baquero, M.B.Sánchez, S.Valdezate, E.Escudero, G.Berg, R.Cantón, F.Baquero, J.C.Galán, and J.L.Martínez (2010).
Polymorphic mutation frequencies of clinical and environmental Stenotrophomonas maltophilia populations.
  Appl Environ Microbiol, 76, 1746-1758.  
  20981145 R.Morita, S.Nakane, A.Shimada, M.Inoue, H.Iino, T.Wakamatsu, K.Fukui, N.Nakagawa, R.Masui, and S.Kuramitsu (2010).
Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems.
  J Nucleic Acids, 2010, 179594.  
20089866 V.V.Hargreaves, S.S.Shell, D.J.Mazur, M.T.Hess, and R.D.Kolodner (2010).
Interaction between the Msh2 and Msh6 nucleotide-binding sites in the Saccharomyces cerevisiae Msh2-Msh6 complex.
  J Biol Chem, 285, 9301-9310.  
19237577 A.Mazurek, C.N.Johnson, M.W.Germann, and R.Fishel (2009).
Sequence context effect for hMSH2-hMSH6 mismatch-dependent activation.
  Proc Natl Acad Sci U S A, 106, 4177-4182.  
19123200 G.Wang, and K.M.Vasquez (2009).
Models for chromosomal replication-independent non-B DNA structure-induced genetic instability.
  Mol Carcinog, 48, 286-298.  
19775280 L.S.Li, J.C.Morales, M.Veigl, D.Sedwick, S.Greer, M.Meyers, M.Wagner, R.Fishel, and D.A.Boothman (2009).
DNA mismatch repair (MMR)-dependent 5-fluorouracil cytotoxicity and the potential for new therapeutic targets.
  Br J Pharmacol, 158, 679-692.  
18854319 I.Tessmer, Y.Yang, J.Zhai, C.Du, P.Hsieh, M.M.Hingorani, and D.A.Erie (2008).
Mechanism of MutS searching for DNA mismatches and signaling repair.
  J Biol Chem, 283, 36646-36654.  
18491151 M.Castellano-Castillo, H.Kostrhunova, V.Marini, J.Kasparkova, P.J.Sadler, J.M.Malinge, and V.Brabec (2008).
Binding of mismatch repair protein MutS to mispaired DNA adducts of intercalating ruthenium(II) arene complexes.
  J Biol Inorg Chem, 13, 993-999.  
18406444 P.Hsieh, and K.Yamane (2008).
DNA mismatch repair: molecular mechanism, cancer, and ageing.
  Mech Ageing Dev, 129, 391-407.  
18673453 S.Acharya (2008).
Mutations in the signature motif in MutS affect ATP-induced clamp formation and mismatch repair.
  Mol Microbiol, 69, 1544-1559.  
18773911 S.N.Huang, and D.M.Crothers (2008).
The role of nucleotide cofactor binding in cooperativity and specificity of MutS recognition.
  J Mol Biol, 384, 31-47.  
18157156 W.Yang (2008).
Structure and mechanism for DNA lesion recognition.
  Cell Res, 18, 184-197.  
17207499 E.Jacobs-Palmer, and M.M.Hingorani (2007).
The effects of nucleotides on MutS-DNA binding kinetics clarify the role of MutS ATPase activity in mismatch repair.
  J Mol Biol, 366, 1087-1098.  
17531815 J.J.Warren, T.J.Pohlhaus, A.Changela, R.R.Iyer, P.L.Modrich, and L.S.Beese (2007).
Structure of the human MutSalpha DNA lesion recognition complex.
  Mol Cell, 26, 579-592.
PDB codes: 2o8b 2o8c 2o8d 2o8e 2o8f
17505105 J.Kondo, T.Sunami, and A.Takénaka (2007).
The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch.
  Acta Crystallogr D Biol Crystallogr, 63, 673-681.
PDB code: 2got
17636021 J.M.Harrington, and R.D.Kolodner (2007).
Saccharomyces cerevisiae Msh2-Msh3 acts in repair of base-base mispairs.
  Mol Cell Biol, 27, 6546-6554.  
16876990 M.Cho, S.Chung, S.D.Heo, J.Ku, and C.Ban (2007).
A simple fluorescent method for detecting mismatched DNAs using a MutS-fluorophore conjugate.
  Biosens Bioelectron, 22, 1376-1381.  
17141577 S.F.Holmes, K.D.Scarpinato, S.D.McCulloch, R.M.Schaaper, and T.A.Kunkel (2007).
Specialized mismatch repair function of Glu339 in the Phe-X-Glu motif of yeast Msh6.
  DNA Repair (Amst), 6, 293-303.  
17573527 S.S.Shell, C.D.Putnam, and R.D.Kolodner (2007).
Chimeric Saccharomyces cerevisiae Msh6 protein with an Msh3 mispair-binding domain combines properties of both proteins.
  Proc Natl Acad Sci U S A, 104, 10956-10961.  
16648361 F.R.Salsbury, J.E.Clodfelter, M.B.Gentry, T.Hollis, and K.D.Scarpinato (2006).
The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response.
  Nucleic Acids Res, 34, 2173-2185.  
16821093 G.Plotz, S.Zeuzem, and J.Raedle (2006).
DNA mismatch repair and Lynch syndrome.
  J Mol Histol, 37, 271-283.  
16407973 J.H.Lebbink, D.Georgijevic, G.Natrajan, A.Fish, H.H.Winterwerp, T.K.Sixma, and N.de Wind (2006).
Dual role of MutS glutamate 38 in DNA mismatch discrimination and in the authorization of repair.
  EMBO J, 25, 409-419.
PDB codes: 1wb9 1wbb 1wbd
16437133 M.Dekker, C.Brouwers, M.Aarts, J.van der Torre, S.de Vries, H.van de Vrugt, and H.te Riele (2006).
Effective oligonucleotide-mediated gene disruption in ES cells lacking the mismatch repair protein MSH3.
  Gene Ther, 13, 686-694.  
16545956 M.Garcia-Diaz, and T.A.Kunkel (2006).
Mechanism of a genetic glissando: structural biology of indel mutations.
  Trends Biochem Sci, 31, 206-214.  
16107880 A.Vaisman, H.Ling, R.Woodgate, and W.Yang (2005).
Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis.
  EMBO J, 24, 2957-2967.
PDB codes: 2ago 2agp 2agq
15709958 D.Kültz (2005).
Molecular and evolutionary basis of the cellular stress response.
  Annu Rev Physiol, 67, 225-257.  
15866941 J.Kang, S.Huang, and M.J.Blaser (2005).
Structural and functional divergence of MutS2 from bacterial MutS1 and eukaryotic MSH4-MSH5 homologs.
  J Bacteriol, 187, 3528-3537.  
15952900 T.A.Kunkel, and D.A.Erie (2005).
DNA mismatch repair.
  Annu Rev Biochem, 74, 681-710.  
16061937 Y.Yang, L.E.Sass, C.Du, P.Hsieh, and D.A.Erie (2005).
Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactions.
  Nucleic Acids Res, 33, 4322-4334.  
14530450 S.Y.Wu, K.Culligan, M.Lamers, and J.Hays (2003).
Dissimilar mispair-recognition spectra of Arabidopsis DNA-mismatch-repair proteins MSH2*MSH6 (MutSalpha) and MSH2*MSH7 (MutSgamma).
  Nucleic Acids Res, 31, 6027-6034.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.