User:Nane Milene Sposito Almeida Pereira/Sandbox 1

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SiaC-SiaD Complex

Crystal structure of diguanylate cyclase SiaD in complex with its activator SiaC from Pseudomonas aeruginosa (PDB entry 7E6G)

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Function

Cyclic dimeric (3'–5') guanosine monophosphate (C-di-GMP) is a bacterial second messenger present in several biological aspects of several environmental and pathogenic bacteria. This second messenger is capable of regulating the cell cycle, biofilm formation, dispersal, motility, and virulence. The synthesis and degradation of c-diGMP are controlled by the activities of two classes of proteins: diguanylate cyclases (DGCs), with an active GGDEF domain, and specific phosphodiesterases (PDEs), with an EAL or HD-GYP domain. SiaD has DGC activity modulated by its binding partner through direct interaction with SiaC, forming the SiaC-SiaD complex ^[1].

Structural highlights

General Aspects

The SiaC-SiaD complex is formed by and the binding of . The conformation of the is composed of two SiaD molecules (SiaD-A and SiaD-B) that form a parallel spiral through their helix rods, and their dimeric rods are stabilized by the binding of two pairs of SiaC molecules (SiaC-C/SiaC-D and SiaC-E/SiaC-F), each in a different location along the dimeric stem, which may be proximal or distal to the DGC domain of SiaD. Furthermore, a non-hydrolyzable GTP analog molecule, , was observed to bind to the active site of SiaD-A.

The crystal structure of full-lenght SiaD in complex with SiaC was determined by integrating the diffraction data and scaling them using the program HKL3000 to space group C2221 at 2.65 Å resolution, and the structure was subsequently determined through molecular replacement using the published conserved DGC domain of the WspR structure (PDB code: 3BRE) and the SiaC structure (PDB code: 6KKP).

The accuracy of SiaC–SiaD complex conformation obtained from the structure was further confirmed using the synchrotron-based solution small angle X-ray scattering (SAXS) and the result suggested consistency between the experimental scattering intensity and the crystal structure model.

The DGC domain of SiaD

The C-terminal GGDEF domain of SiaD is highly conserved. Two DGC domains in the complex are oriented anti-parallel, with their active sites facing each other. Each DGC domain consists of a core canonical fold of five antiparallel β-strands (β1–β5) around which five α-helices (α0–α4) and two short antiparallel β-strands are wrapped (β3ʹ and β3"), forming a highly conserved GTP substrate-binding site (GGDEF domain, A-site) and a c-di-GMP product binding/inhibitory site (I-site).

Overview of the DGC domain dimer. A-site and I-site were labeled, respectively [1]

Furthermore, residues involved in GTP and Mg 2+ binding have been shown to be essential for the DGC activity of SiaD.

GpCpp binds to the C-terminal DGC domain of SiaD (A-site) [1]

References

↑ Chen G, Zhou J, Zuo Y, Huo W, Peng J, Li M, Zhang Y, Wang T, Zhang L, Zhang L, Liang H. Structural basis for diguanylate cyclase activation by its binding partner in Pseudomonas aeruginosa. Elife. 2021 Sep 9;10:e67289. PMID:34498587 doi:10.7554/eLife.67289

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Nane Milene Sposito Almeida Pereira

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 '''The DGC domain of SiaD'''
-The C-terminal GGDEF domain of SiaD is highly conserved. Two DGC domains in the complex are oriented anti-parallel, with their active sites facing each other. Each DGC domain consists of a core canonical fold of five antiparallel β-strands (β1–β5) around which five α-helices (α0–α4) and two short antiparallel β-strands are wrapped (β3ʹ and β3"), forming a highly conserved GTP substrate-binding site (GGDEF domain, A-site) and a c-di-GMP product binding/inhibitory site (I-site). [[Image:Overview_of_the_DGC_domain_dimer.jpg|500px|left|thumb| Overview of the DGC domain dimer. A-site and I-site were labeled, respectively [3]]]
+The C-terminal GGDEF domain of SiaD is highly conserved. Two DGC domains in the complex are oriented anti-parallel, with their active sites facing each other. Each DGC domain consists of a core canonical fold of five antiparallel β-strands (β1–β5) around which five α-helices (α0–α4) and two short antiparallel β-strands are wrapped (β3ʹ and β3"), forming a highly conserved GTP substrate-binding site (GGDEF domain, A-site) and a c-di-GMP product binding/inhibitory site (I-site). [[Image:Overview_of_the_DGC_domain_dimer.jpg|500px|left|thumb| Overview of the DGC domain dimer. A-site and I-site were labeled, respectively [1]]]
-Furthermore, residues involved in GTP and Mg 2+ binding have been shown to be essential for the DGC activity of SiaD. [[Image:GpCpp_SiaD_(A-site).jpg|220px|center|thumb| GpCpp binds to the C-terminal DGC domain of SiaD (A-site) [3]]]
+Furthermore, residues involved in GTP and Mg 2+ binding have been shown to be essential for the DGC activity of SiaD. [[Image:GpCpp_SiaD_(A-site).jpg|220px|center|thumb| GpCpp binds to the C-terminal DGC domain of SiaD (A-site) [1]]]

User:Nane Milene Sposito Almeida Pereira/Sandbox 1

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Current revision

SiaC-SiaD Complex

Function

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References

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