PDBsum entry 1nhj

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Replication, signaling protein PDB id
Jmol PyMol
Protein chain
333 a.a. *
Waters ×201
* Residue conservation analysis
PDB id:
Name: Replication, signaling protein
Title: Crystal structure of n-terminal 40kd mutl/a100p mutant prote with adpnp and one sodium
Structure: DNA mismatch repair protein mutl. Chain: a. Fragment: n-terminal 40kd atpase fragment (ln40). Engineered: yes. Mutation: yes
Source: Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: mutl. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
2.30Å     R-factor:   0.217     R-free:   0.266
Authors: X.Hu,M.Machius,W.Yang
Key ref:
X.Hu et al. (2003). Monovalent cation dependence and preference of GHKL ATPases and kinases. FEBS Lett, 544, 268-273. PubMed id: 12782329 DOI: 10.1016/S0014-5793(03)00519-2
19-Dec-02     Release date:   10-Jun-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P23367  (MUTL_ECOLI) -  DNA mismatch repair protein MutL
615 a.a.
333 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     mismatch repair   1 term 
  Biochemical function     ATP binding     2 terms  


DOI no: 10.1016/S0014-5793(03)00519-2 FEBS Lett 544:268-273 (2003)
PubMed id: 12782329  
Monovalent cation dependence and preference of GHKL ATPases and kinases.
X.Hu, M.Machius, W.Yang.
The GHKL phosphotransferase superfamily, characterized by four sequence motifs that form the ATP-binding site, consists of the ATPase domains of type II DNA topoisomerases, Hsp90, and MutL, and bacterial and mitochondrial protein kinases. In addition to a magnesium ion, which is essential for catalysis, a potassium ion bound adjacent to the triphosphate moiety of ATP in a rat mitochondrial protein kinase, BCK (branched-chain alpha-ketoacid dehydrogenase kinase), has been shown to be indispensable for nucleotide binding and hydrolysis. Using X-ray crystallographic, biochemical, and genetic analyses, we find that the monovalent cation-binding site is conserved in MutL, but both Na(+) and K(+) support the MutL ATPase activity. When Ala100 of MutL is substituted by proline, mimicking the K(+)-binding environment in BCK, the mutant MutL protein becomes exclusively dependent on Na(+) for the ATPase activity. The coordination of this Na(+) ion is identical to that of the K(+) ion in BCK and involves four carbonyl oxygen atoms emanating from the hinges of the ATP lid and a non-bridging oxygen of the bound nucleotide. A similar monovalent cation-binding site is found in DNA gyrase with additional coordination by a serine side chain. The conserved and protein-specific monovalent cation-binding site is unique to the GHKL superfamily and probably essential for both ATPase and kinase activity. Dependence on different monovalent cations for catalysis may be exploited for future drug design specifically targeting each individual member of the GHKL superfamily.
  Selected figure(s)  
Figure 2.
Fig. 2. Crystal structures of the ATP-binding site of the WT LN40, BCK and LN40(A100P). a: The active site configuration of the LN40–ADPnP complex in the presence of Mg^2+ and K^+. Peaks above 3σ in an anomalous difference Fourier map are contoured in light blue. b: The ATPγS bound BCK. c: The active site configuration of the LN40(A100P)–ADPnP complex. The ATP analogs (ADPnP and ATPγS) are shown in yellow bonds, the protein carbonyl groups in gray bonds, the Mg^2+ ion is shown in dark green, Na^+ ion in light blue, and K^+ ion dark purple. Coordination of the monovalent cation is highlighted in dark pink.
Figure 3.
Fig. 3. Comparison of the monovalent ion-binding site of BCK, MutL, GyrB, human Hsp90 and CheA. Secondary structures surrounding the ATP-binding site are shown in gray ribbon drawings including motifs I (N) and IV; motif II (G1) and the N- and C-terminal (motif III) hinges of ATP lid are drawn in yellow. For clarity, the connecting part of the ATP lid is not shown. The bound nucleotides are shown in ball-and-stick models, divalent and monovalent cations are shown as cyan and purple spheres, and water oxygens as red sphere.
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2003, 544, 268-273) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18206974 E.J.Sacho, F.A.Kadyrov, P.Modrich, T.A.Kunkel, and D.A.Erie (2008).
Direct visualization of asymmetric adenine-nucleotide-induced conformational changes in MutL alpha.
  Mol Cell, 29, 112-121.  
18400751 K.Richter, J.Soroka, L.Skalniak, A.Leskovar, M.Hessling, J.Reinstein, and J.Buchner (2008).
Conserved conformational changes in the ATPase cycle of human Hsp90.
  J Biol Chem, 283, 17757-17765.  
16267046 E.Di Cera (2006).
A structural perspective on enzymes activated by monovalent cations.
  J Biol Chem, 281, 1305-1308.  
15849317 D.Gadelle, C.Bocs, M.Graille, and P.Forterre (2005).
Inhibition of archaeal growth and DNA topoisomerase VI activities by the Hsp90 inhibitor radicicol.
  Nucleic Acids Res, 33, 2310-2317.  
15105144 S.Bellon, J.D.Parsons, Y.Wei, K.Hayakawa, L.L.Swenson, P.S.Charifson, J.A.Lippke, R.Aldape, and C.H.Gross (2004).
Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase.
  Antimicrob Agents Chemother, 48, 1856-1864.
PDB codes: 1s14 1s16
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