User:Nane Milene Sposito Almeida Pereira/Sandbox 1
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==SiaC-SiaD Complex== | ==SiaC-SiaD Complex== | ||
<StructureSection load='7E6G' size='340' side='right' caption='Crystal structure of diguanylate cyclase SiaD in complex with its activator SiaC from Pseudomonas aeruginosa (PDB entry 7E6G)' scene=''> | <StructureSection load='7E6G' size='340' side='right' caption='Crystal structure of diguanylate cyclase SiaD in complex with its activator SiaC from Pseudomonas aeruginosa (PDB entry 7E6G)' scene=''> | ||
| - | This is a default text for your page '''Nane Milene Sposito Almeida Pereira/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | ||
| - | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | ||
== Function == | == Function == | ||
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'''General Aspects''' | '''General Aspects''' | ||
| - | The SiaC-SiaD complex is formed by two SiaD molecules and the binding of four SiaC. The conformation of the complex is composed of two SiaD molecules (<font color="MediumSeaGreen">SiaD-A</font> and <font color="RoyalBlue">SiaD-B</font>) that form a parallel spiral through their helix rods, and their dimeric rods are stabilized by the binding of two pairs of SiaC molecules (<font color="Violet">SiaC-C</font>/<font color="yellow">SiaC-D</font> and <font color="MediumOrchid">SiaC-E</font>/<font color="SkyBlue">SiaC-F</font>), 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, GpCpp, was observed to bind to the active site of SiaD-A. | + | The SiaC-SiaD complex is formed by <scene name='97/973098/Siad/1'>two SiaD molecules</scene> and the binding of <scene name='97/973098/Siac/1'>four SiaC</scene>. The conformation of the <scene name='97/973098/Complex/1'>complex</scene> is composed of two SiaD molecules (<font color="MediumSeaGreen">SiaD-A</font> and <font color="RoyalBlue">SiaD-B</font>) that form a parallel spiral through their helix rods, and their dimeric rods are stabilized by the binding of two pairs of SiaC molecules (<font color="Violet">SiaC-C</font>/<font color="yellow">SiaC-D</font> and <font color="MediumOrchid">SiaC-E</font>/<font color="SkyBlue">SiaC-F</font>), 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, <scene name='97/973098/Gpcpp/1'>GpCpp</scene>, 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 | + | 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. |
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| - | + | '''The DGC domain of SiaD''' | |
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| + | 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) [1]]] | ||
| - | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | ||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
SiaC-SiaD Complex
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![Overview of the DGC domain dimer. A-site and I-site were labeled, respectively [1]](/wiki/index.php/Image:Overview_of_the_DGC_domain_dimer.jpg)
![GpCpp binds to the C-terminal DGC domain of SiaD (A-site) [1]](/wiki/index.php/Image:GpCpp_SiaD_%28A-site%29.jpg)
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
