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Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis.

TitleStructural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis.
Publication TypeJournal Article
Year of Publication2012
AuthorsDago, AE, Schug, A, Procaccini, A, Hoch, JA, Weigt, M, Szurmant, H
JournalProc Natl Acad Sci U S A
Date Published2012 Jun 26
KeywordsBacillus subtilis, Genomics, Models, Molecular, Mutagenesis, Site-Directed, Phosphorylation, Protein Conformation, Protein Kinases

Signal transduction proteins such as bacterial sensor histidine kinases, designed to transition between multiple conformations, are often ruled by unstable transient interactions making structural characterization of all functional states difficult. This study explored the inactive and signal-activated conformational states of the two catalytic domains of sensor histidine kinases, HisKA and HATPase. Direct coupling analyses, a global statistical inference approach, was applied to >13,000 such domains from protein databases to identify residue contacts between the two domains. These contacts guided structural assembly of the domains using MAGMA, an advanced molecular dynamics docking method. The active conformation structure generated by MAGMA simultaneously accommodated the sequence derived residue contacts and the ATP-catalytic histidine contact. The validity of this structure was confirmed biologically by mutation of contact positions in the Bacillus subtilis sensor histidine kinase KinA and by restoration of activity in an inactive KinA(HisKA):KinD(HATPase) hybrid protein. These data indicate that signals binding to sensor domains activate sensor histidine kinases by causing localized strain and unwinding at the end of the C-terminal helix of the HisKA domain. This destabilizes the contact positions of the inactive conformation of the two domains, identified by previous crystal structure analyses and by the sequence analysis described here, inducing the formation of the active conformation. This study reveals that structures of unstable transient complexes of interacting proteins and of protein domains are accessible by applying this combination of cross-validating technologies.

Alternate JournalProc. Natl. Acad. Sci. U.S.A.
PubMed ID22670053
PubMed Central IDPMC3387055
Grant ListAI055860 / AI / NIAID NIH HHS / United States
GM019416 / GM / NIGMS NIH HHS / United States
R01 GM019416 / GM / NIGMS NIH HHS / United States