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Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli.

Fan H, Hahm J, Diggs S, Perry JJ, Blaha G - J. Biol. Chem. (2015)

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.

View Article: PubMed Central - PubMed

Affiliation: From the Department of Biochemistry, University of California, Riverside, California 92521.

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Related in: MedlinePlus

Binding of GDP and ppGpp to full-length BipA.A, overview of the GDP-bound BipA structure. The protein is rendered as a schematic with the domains colored as in Fig. 1. The bound GDP molecule is rendered as a space-filling model and colored green. B, close-up view of the GDP binding pocket in domain I. Residues of protein 128NKVD131, 166SAL168, and 15DHGKT19 form the binding pocket for GDP and are displayed in red. The bound GDP is in green, and the bound magnesium ion is represented as a green sphere. C, superposition of domain I of the GDP-bound and of the ppGpp-bound structures. The GDP-bound form is displayed in red, and the ppGpp-bound form is in blue. D, superposition of domain I of GDP-bound EF-G and ppGpp-bound BipA structures. EF-G domains I and G′ are displayed in red and orange, and the BipA domain I is in blue.
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Figure 3: Binding of GDP and ppGpp to full-length BipA.A, overview of the GDP-bound BipA structure. The protein is rendered as a schematic with the domains colored as in Fig. 1. The bound GDP molecule is rendered as a space-filling model and colored green. B, close-up view of the GDP binding pocket in domain I. Residues of protein 128NKVD131, 166SAL168, and 15DHGKT19 form the binding pocket for GDP and are displayed in red. The bound GDP is in green, and the bound magnesium ion is represented as a green sphere. C, superposition of domain I of the GDP-bound and of the ppGpp-bound structures. The GDP-bound form is displayed in red, and the ppGpp-bound form is in blue. D, superposition of domain I of GDP-bound EF-G and ppGpp-bound BipA structures. EF-G domains I and G′ are displayed in red and orange, and the BipA domain I is in blue.

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).


Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli.

Fan H, Hahm J, Diggs S, Perry JJ, Blaha G - J. Biol. Chem. (2015)

Binding of GDP and ppGpp to full-length BipA.A, overview of the GDP-bound BipA structure. The protein is rendered as a schematic with the domains colored as in Fig. 1. The bound GDP molecule is rendered as a space-filling model and colored green. B, close-up view of the GDP binding pocket in domain I. Residues of protein 128NKVD131, 166SAL168, and 15DHGKT19 form the binding pocket for GDP and are displayed in red. The bound GDP is in green, and the bound magnesium ion is represented as a green sphere. C, superposition of domain I of the GDP-bound and of the ppGpp-bound structures. The GDP-bound form is displayed in red, and the ppGpp-bound form is in blue. D, superposition of domain I of GDP-bound EF-G and ppGpp-bound BipA structures. EF-G domains I and G′ are displayed in red and orange, and the BipA domain I is in blue.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4543647&req=5

Figure 3: Binding of GDP and ppGpp to full-length BipA.A, overview of the GDP-bound BipA structure. The protein is rendered as a schematic with the domains colored as in Fig. 1. The bound GDP molecule is rendered as a space-filling model and colored green. B, close-up view of the GDP binding pocket in domain I. Residues of protein 128NKVD131, 166SAL168, and 15DHGKT19 form the binding pocket for GDP and are displayed in red. The bound GDP is in green, and the bound magnesium ion is represented as a green sphere. C, superposition of domain I of the GDP-bound and of the ppGpp-bound structures. The GDP-bound form is displayed in red, and the ppGpp-bound form is in blue. D, superposition of domain I of GDP-bound EF-G and ppGpp-bound BipA structures. EF-G domains I and G′ are displayed in red and orange, and the BipA domain I is in blue.
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).

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.

View Article: PubMed Central - PubMed

Affiliation: From the Department of Biochemistry, University of California, Riverside, California 92521.

Show MeSH
Related in: MedlinePlus