The structure of the KinA-Sda complex suggests an allosteric mechanism of histidine kinase inhibition.

The Bacillus subtilis histidine kinase KinA controls activation of the transcription factor governing sporulation, Spo0A. The decision to sporulate involves KinA phosphorylating itself on a conserved histidine residue, after which the phosphate moiety is relayed via two other proteins to Spo0A. The DNA-damage checkpoint inhibitor Sda halts this pathway by binding KinA and blocking the autokinase reaction. We have performed small-angle X-ray scattering and neutron contrast variation studies on the complex formed by KinA and Sda. The data show that two Sda molecules bind to the base of the DHp dimerization domain of the KinA dimer. In this position Sda does not appear to be able to sterically block the catalytic domain from accessing its target histidine, as previously proposed, but rather may effect an allosteric mode of inhibition involving transmission of the inhibitory signal via the four-helix bundle that forms the DHp domain.

[1]  G L Hazelbauer,et al.  Transmembrane signaling in bacterial chemoreceptors. , 2001, Trends in biochemical sciences.

[2]  Mitsuhiko Ikura,et al.  NMR structure of the histidine kinase domain of the E. coli osmosensor EnvZ , 1998, Nature.

[3]  I. Kurtser,et al.  Replication Initiation Proteins Regulate a Developmental Checkpoint in Bacillus subtilis , 2001, Cell.

[4]  P. S. Kim,et al.  Imitation of Escherichia coli Aspartate Receptor Signaling in Engineered Dimers of the Cytoplasmic Domain , 1996, Science.

[5]  C. Chothia,et al.  The Packing Density in Proteins: Standard Radii and Volumes , 1999 .

[6]  D. Svergun,et al.  CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates , 1995 .

[7]  J. Trewhella,et al.  Troponin I encompasses an extended troponin C in the Ca(2+)-bound complex: a small-angle X-ray and neutron scattering study. , 1994, Biochemistry.

[8]  Dmitri I. Svergun,et al.  PRIMUS: a Windows PC-based system for small-angle scattering data analysis , 2003 .

[9]  Dmitri I. Svergun,et al.  Determination of the regularization parameter in indirect-transform methods using perceptual criteria , 1992 .

[10]  Yan Zhu,et al.  Solution structure of the homodimeric core domain of Escherichia coli histidine kinase EnvZ , 1999, Nature Structural Biology.

[11]  D. Svergun,et al.  Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution , 2006, European Biophysics Journal.

[12]  W A Hendrickson,et al.  Structural and Mutational Analysis of the PhoQ Histidine Kinase Catalytic Domain , 2001, The Journal of Biological Chemistry.

[13]  Wayne A Hendrickson,et al.  Structure of the entire cytoplasmic portion of a sensor histidine‐kinase protein , 2005, The EMBO journal.

[14]  J. Trewhella,et al.  Comparison of the crystal and solution structures of calmodulin and troponin C. , 1988, Biochemistry.

[15]  William J. Orts,et al.  The 30 m Small-Angle Neutron Scattering Instruments at the National Institute of Standards and Technology , 1998 .

[16]  J. Hoch,et al.  Two-component and phosphorelay signal transduction. , 2000, Current opinion in microbiology.

[17]  M. Inouye,et al.  Probing catalytically essential domain orientation in histidine kinase EnvZ by targeted disulfide crosslinking. , 2003, Journal of molecular biology.

[18]  H. Sugimoto,et al.  The signaling pathway in histidine kinase and the response regulator complex revealed by X-ray crystallography and solution scattering. , 2006, Journal of molecular biology.

[19]  D I Svergun,et al.  Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. , 1999, Biophysical journal.

[20]  C. Sander,et al.  Dali: a network tool for protein structure comparison. , 1995, Trends in biochemical sciences.

[21]  Steven R. Kline,et al.  Reduction and analysis of SANS and USANS data using IGOR Pro , 2006 .

[22]  B. Schoenborn,et al.  Asymmetry in the 50S ribosomal subunit of Escherichia coli. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[23]  I. Zhulin,et al.  PAS Domains: Internal Sensors of Oxygen, Redox Potential, and Light , 1999, Microbiology and Molecular Biology Reviews.

[24]  I. Tsigelny,et al.  The Crystal Structure of Beryllofluoride Spo0F in Complex with the Phosphotransferase Spo0B Represents a Phosphotransfer Pretransition State† , 2006, Journal of bacteriology.

[25]  Dmitri I Svergun,et al.  Global rigid body modeling of macromolecular complexes against small-angle scattering data. , 2005, Biophysical journal.

[26]  J. Hoch,et al.  A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction. , 2000, Structure.

[27]  P. Tucker,et al.  Structural and functional aspects of the sensor histidine kinase PrrB from Mycobacterium tuberculosis. , 2006, Structure.

[28]  Mark W Maciejewski,et al.  Structure and mechanism of action of Sda, an inhibitor of the histidine kinases that regulate initiation of sporulation in Bacillus subtilis. , 2004, Molecular cell.

[29]  K. Ibel.  Comparison of neutron and X-ray scattering of dilute myoglobin solutions. , 1975, Journal of molecular biology.

[30]  D. Hilbert,et al.  Sporulation of Bacillus subtilis. , 2004, Current opinion in microbiology.

[31]  A. Guinier,et al.  La diffraction des rayons X aux très petits angles : application à l'étude de phénomènes ultramicroscopiques , 1939 .

[32]  M. Brillouin,et al.  La diffraction des rayons X aux très petits angles: application a l'étude de phénomènes ultramicroscopiques , 1939 .

[33]  K. Katoh,et al.  MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.

[34]  M. Simon,et al.  Structure of CheA, a Signal-Transducing Histidine Kinase , 1999, Cell.

[35]  A. Ninfa,et al.  Crystal structure of the C-terminal domain of the two-component system transmitter protein nitrogen regulator II (NRII; NtrB), regulator of nitrogen assimilation in Escherichia coli. , 2004, Biochemistry.

[36]  G. Porod,et al.  Die Röntgenkleinwinkelstreuung von dichtgepackten kolloiden Systemen , 1951 .