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Transferase/transferase inhibitor PDB id
3d36
Jmol
Contents
Protein chains
217 a.a. *
42 a.a. *
Ligands
ADP ×2
MPD ×4
Metals
_MG ×2
Waters ×373
* Residue conservation analysis
PDB id:
3d36
Name: Transferase/transferase inhibitor
Title: How to switch off a histidine kinase: crystal structure of geobacillus stearothermophilus kinb with the inhibitor sda
Structure: Sporulation kinase b. Chain: a, b. Engineered: yes. Sporulation kinase inhibitor sda. Chain: c. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 272567. Strain: 10. Gene: gk1832, gka09. Expressed in: escherichia coli. Gene: gk2527.
Resolution:
2.03Å     R-factor:   0.201     R-free:   0.215
Authors: M.J.Bick,V.Lamour,K.R.Rajashankar,Y.Gordiyenko,C.V.Robinson, S.A.Darst
Key ref:
M.J.Bick et al. (2009). How to Switch Off a Histidine Kinase: Crystal Structure of Geobacillus stearothermophilus KinB with the inhibitor Sda. J Mol Biol, 386, 163-177. PubMed id: 19101565 DOI: 10.1016/j.jmb.2008.12.006
Date:
09-May-08     Release date:   13-Jan-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.2.7.13.3  - Histidine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP
 + protein L-histidine
 = ADP
 + protein N-phospho-L-histidine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2008.12.006 J Mol Biol 386:163-177 (2009)
PubMed id: 19101565  
 
 
How to Switch Off a Histidine Kinase: Crystal Structure of Geobacillus stearothermophilus KinB with the inhibitor Sda.
M.J.Bick, V.Lamour, K.R.Rajashankar, Y.Gordiyenko, C.V.Robinson, S.A.Darst.
 
  ABSTRACT  
 
Entry to sporulation in bacilli is governed by a histidine kinase phosphorelay, a variation of the predominant signal transduction mechanism in prokaryotes. Sda directly inhibits sporulation histidine kinases in response to DNA damage and replication defects. We determined a 2.0-A-resolution X-ray crystal structure of the intact cytoplasmic catalytic core [comprising the dimerization and histidine phosphotransfer domain (DHp domain), connected to the ATP binding catalytic domain] of the Geobacillus stearothermophilus sporulation kinase KinB complexed with Sda. Structural and biochemical analyses reveal that Sda binds to the base of the DHp domain and prevents molecular transactions with the DHp domain to which it is bound by acting as a simple molecular barricade. Sda acts to sterically block communication between the catalytic domain and the DHp domain, which is required for autophosphorylation, as well as to sterically block communication between the response regulator Spo0F and the DHp domain, which is required for phosphotransfer and phosphatase activities.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The Gst Sda/KinB-CC complex. (a) Schematic diagram illustrating the structural features of the Bacillus sporulation HK KinB. The colored domains (DHp and CA domains) comprising the cytoplasmic CC have been crystallized in this study. The HK functions as a homodimer (one monomer is shown in dark red; the other is shown in orange). Autophosphorylation occurs in trans, with the orange CA domain phosphorylating the phosphoacceptor His residue (labeled “H”) of the red DHp domain. (b) Sda inhibits spontaneous autophosphorylation of KinB-CC. Incubation of KinB-CC with γ-[^32P]ATP results in autophosphorylation, as monitored by SDS-PAGE and PhosphorImager (lane 1). Addition of increasing concentrations of Sda (1-fold, 5-fold, or 25-fold molar excess over KinB-CC for lanes 2–4, respectively) inhibits the autophosphorylation reaction. (c) Structure of the Sda/KinB-CC complex. Ribbon diagrams, with each protein chain color-coded: KinB-CC monomer A, dark red; KinB-CC monomer B, orange; Sda, blue. The KinB DHp and CA domains are labeled. ADP molecules bound to the CA domains are shown in stick format, with carbon atoms shown in yellow. The associated Mg^2 + are shown as gray spheres. The side chain of the phosphoacceptor His213 is also shown. Disordered segments near the N-terminus of the KinB monomers are shown as spheres. 		Figure 6.
Fig. 6. Mechanism of the Sda inhibition of autophosphorylation and phosphotransfer. (a) Mechanism of the Sda inhibition of autophosphorylation. The KinB DHp domain is shown as a ribbon diagram, with the side chain of the phosphoacceptor His213. Sda is shown in stick format. Superimposed on the Sda/KinB DHp structure is a KinB CA domain (shown in stick format, but with the ADP and Mg^2 + shown as CPK spheres) poised for the autophosphorylation reaction (modeled according to Marina et al.^14). Sda is shown in blue, except for atoms within 4 Å of the modeled CA domain, which are shown in green. The KinB CA domain is shown in orange, except for atoms within 4 Å of Sda, which are shown in magenta. The green and magenta atoms on Sda and KinB CA, respectively, illustrate the extent of the steric clash between the bound Sda and the modeled CA domain, indicating that phosphorylation of His213 by the CA domain would be sterically blocked by the bound Sda. (b) Mechanism of the Sda inhibition of phosphotransfer to Spo0F. Sda (blue) and the KinB DHp domain (dark red and orange) are shown as ribbon diagrams, with the side chain of His213. Superimposed on the Sda/KinB DHp structure is Spo0F (yellow ribbon, with the side chain of the phosphoacceptor Asp54) poised for phosphotransfer (modeled on the Spo0F/Spo0B crystal structure^27). Extensive steric overlap between Sda and Spo0F indicates that the phosphotransfer reaction would be sterically blocked by the bound Sda.
 
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2009, 386, 163-177) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21342783 E.C.Hobbs, F.Fontaine, X.Yin, and G.Storz (2011).
An expanding universe of small proteins.
  Curr Opin Microbiol, 14, 167-173.  
20120026 D.A.Jacques, and J.Trewhella (2010).
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  Protein Sci, 19, 642-657.  
19943903 D.R.Buelow, and T.L.Raivio (2010).
Three (and more) component regulatory systems - auxiliary regulators of bacterial histidine kinases.
  Mol Microbiol, 75, 547-566.  
20453099 P.D.Scheu, Y.F.Liao, J.Bauer, H.Kneuper, T.Basché, G.Unden, and W.Erker (2010).
Oligomeric sensor kinase DcuS in the membrane of Escherichia coli and in proteoliposomes: chemical cross-linking and FRET spectroscopy.
  J Bacteriol, 192, 3474-3483.  
19966007 V.Stewart, and L.L.Chen (2010).
The S helix mediates signal transmission as a HAMP domain coiled-coil extension in the NarX nitrate sensor from Escherichia coli K-12.
  J Bacteriol, 192, 734-745.  
19465772 D.A.Jacques, M.Streamer, S.L.Rowland, G.F.King, J.M.Guss, J.Trewhella, and D.B.Langley (2009).
Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state.
  Acta Crystallogr D Biol Crystallogr, 65, 574-581.
PDB code: 3fyr
19805278 D.Albanesi, M.Martín, F.Trajtenberg, M.C.Mansilla, A.Haouz, P.M.Alzari, D.de Mendoza, and A.Buschiazzo (2009).
Structural plasticity and catalysis regulation of a thermosensor histidine kinase.
  Proc Natl Acad Sci U S A, 106, 16185-16190.
PDB codes: 3ehf 3ehh 3ehj 3gie 3gif 3gig
19800110 P.Casino, V.Rubio, and A.Marina (2009).
Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction.
  Cell, 139, 325-336.
PDB codes: 3dge 3dgf 3gl9
19561131 P.Eswaramoorthy, T.Guo, and M.Fujita (2009).
In vivo domain-based functional analysis of the major sporulation sensor kinase, KinA, in Bacillus subtilis.
  J Bacteriol, 191, 5358-5368.  
19575571 R.Gao, and A.M.Stock (2009).
Biological insights from structures of two-component proteins.
  Annu Rev Microbiol, 63, 133-154.  
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