User:Tilman Schirmer/Sandbox 211

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After binding of the <scene name='User:Tilman_Schirmer/Sandbox_211/Competent_ggdef_dimer/6'>GTP substrate</scene> (here we show GMP, <s>please update</s>), it is believed that two GGDEF domains associate antiparallely to form a catalytically competent dimer (<scene name='User:Tilman_Schirmer/Sandbox_211/Competent_ggdef_dimer/3'>view1</scene>, <scene name='User:Tilman_Schirmer/Sandbox_211/Competent_ggdef_dimer/1'>view2</scene>). Then, by inter-molecular nucleophilic in-line attack of the O3' atom onto the α-phosphorous of the other GTP substrate molecule, two phosphodiester bonds are formed under release of two pyrophosphate molecules (2 GTP -> c-di-GMP + 2 PPi).
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After binding of the <scene name='User:Tilman_Schirmer/Sandbox_211/Competent_ggdef_dimer/6'>GTP substrate</scene> (here we show GMP, <i>please update</i>), it is believed that two GGDEF domains associate antiparallely to form a catalytically competent dimer (<scene name='User:Tilman_Schirmer/Sandbox_211/Competent_ggdef_dimer/3'>view1</scene>, <scene name='User:Tilman_Schirmer/Sandbox_211/Competent_ggdef_dimer/1'>view2</scene>). Then, by inter-molecular nucleophilic in-line attack of the O3' atom onto the α-phosphorous of the other GTP substrate molecule, two phosphodiester bonds are formed under release of two pyrophosphate molecules (2 GTP -> c-di-GMP + 2 PPi).

Revision as of 08:06, 15 July 2009

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PleD

Overview

Diguanylate cyclase PleD (1w25)

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from Caulobacter crescentus is a response regulator with an unorthodox catalytic, diguanylate cyclase, output domain. It is composed of a canonical CheY-like response regulator receiver () domain, a Rec-like () adaptor domain, and a C-terminal domain that confers the catalytic acitvity.



The GGDEF domain is named after the highly conserved (in PleD it is GGEEF) that locates to a β-hairpin.












Substrate binding

Diguanylate cyclase PleD (2v0n)

Drag the structure with the mouse to rotate


The motif is part of the as identified in the structure of PleD in complex with . The GGDEF domain binds only one GTP substrate molecule. For the reaction to proceed, two GTP loaded GGDEF domains have to align antiparallely.





Complete active site

Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.

After binding of the (here we show GMP, please update), it is believed that two GGDEF domains associate antiparallely to form a catalytically competent dimer (, ). Then, by inter-molecular nucleophilic in-line attack of the O3' atom onto the α-phosphorous of the other GTP substrate molecule, two phosphodiester bonds are formed under release of two pyrophosphate molecules (2 GTP -> c-di-GMP + 2 PPi).

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Tilman Schirmer

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