Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli.
Bottom Line: The crystal structure and small-angle x-ray scattering data of the protein with bound nucleotides, together with a thermodynamic analysis of the binding of GDP and of ppGpp to BipA, indicate that the ppGpp-bound form of BipA adopts the structure of the GDP form.This suggests furthermore, that the switch in binding preference only occurs when both ppGpp and the small ribosomal subunit are present.This molecular mechanism would allow BipA to interact with both the ribosome and the small ribosomal subunit during stress response.
Affiliation: From the Department of Biochemistry, University of California, Riverside, California 92521.Show MeSH
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Mentions: The structure of BipA with bound GDP is very similar to that of the apo form with a root mean square deviation (r.m.s.d.) of 0.49 Å across all matching main chain atoms. The GDP nucleotide is bound in domain I (Fig. 3A) in similar way as in other translational GTPases. The binding pocket for the nucleotide's base is composed of the conserved sequence motifs NKVD (residues 128–131) and SAL (residues 166–168). These residues provide hydrogen bonds and hydrophobic interactions for the selective binding of the base. The conserved residues of the G1-box sequence motif (residues 12AHVDHGKT19) wrap around the phosphate groups of GDP with the side chain of Asp15 coordinating a magnesium ion that in turn coordinates to both phosphates of GDP (Fig. 3B). The “switch 1” region of BipA (residues 42–65), whose position is affected by the γ-phosphate of GTP in other GTPases, is disordered (30).
Affiliation: From the Department of Biochemistry, University of California, Riverside, California 92521.