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User:Tilman Schirmer/Sandbox 201
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< User:Tilman Schirmer(Difference between revisions)
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[[User:Tilman_Schirmer/Sandbox_200|back]] | [[User:Tilman_Schirmer/Sandbox_200|back]] | ||
| - | + | '''PleD''' | |
| - | === | + | ===Overview=== |
| + | |||
| + | <applet load='1w25' scene='User:Tilman_Schirmer/Sandbox_201/Protomer/5' size='300' frame='true' align='right' caption='Diguanylate cyclase PleD (1w25)' /> | ||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer/5'>PleD</scene> | + | <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer/5'>PleD</scene> 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 (<scene name='User:Tilman_Schirmer/Sandbox_201/Protomer/7'>Rec</scene>) domain, |
| - | + | a Rec-like (<scene name='User:Tilman_Schirmer/Sandbox_201/Protomer_rec_prime/2'>Rec'</scene>) adaptor domain, | |
| - | a Rec-like (scene name='User:Tilman_Schirmer/Sandbox_201/Protomer_rec_prime/2'>Rec'</scene>) adaptor domain, | + | |
and a C-terminal <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer_ggdef/1'>GGDEF</scene> domain that confers the catalytic acitvity. | and a C-terminal <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer_ggdef/1'>GGDEF</scene> domain that confers the catalytic acitvity. | ||
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[[Image:Pled_domains_1.jpg|left]] | [[Image:Pled_domains_1.jpg|left]] | ||
| - | <applet load='1w25' scene='User:Tilman_Schirmer/Sandbox_201/Protomer/5' size='300' frame='true' align='right' caption='Diguanylate cyclase PleD (1w25)' /> | ||
| + | The GGDEF domain is named after the highly conserved <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer_ggdef/2'>signature motif </scene> (in PleD it is GGEEF) that locates to a β-hairpin. | ||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer/5'>Protomer</scene> | ||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer/7'>Rec</scene> | ||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer_rec_prime/2'>Rec'</scene> | ||
| - | < | + | <br><br><br><br><br><br><br><br><br> |
| - | + | ===Substrate binding=== | |
| - | == | + | <applet load='2v0n' scene='User:Tilman_Schirmer/Sandbox_201/Substrate_binding_site/4' size='300' frame='true' align='right' caption='Diguanylate cyclase PleD (2v0n)' /> |
| - | <applet load='2v0n' scene='User:Tilman_Schirmer/Sandbox_201/Substrate_binding_site/2' size='300' frame='true' align='right' caption='2v0n' /> | ||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Substrate_binding_site/ | + | The motif is part of the <scene name='User:Tilman_Schirmer/Sandbox_201/Substrate_binding_site/5'>substrate binding site</scene> as identified in the structure of PleD in complex with <scene name='User:Tilman_Schirmer/Sandbox_201/Gtp-a-s/2'>GTP-alpha-S / Mg++</scene>. The GGDEFY domain binds only '''one''' GTP subsrate molecule. For the reaction to proceed, '''two''' GTP loaded GGDEF domains have to align antiparallely. MODEL. |
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Substrate_binding_ctp-a-s_mg/3'>Substrate binding site + ligand (CTP-alpha-S) + Mg++</scene> | ||
| - | <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> | ||
| - | == Allosteric product binding site == | + | |
| + | <br><br><br><br><br><br><br><br><br><br><br><br><br> | ||
| + | |||
| + | === Allosteric product binding site === | ||
<applet load='2v0n' scene='User:Tilman_Schirmer/Sandbox_201/5gp/1' size='300' frame='true' align='right' caption='Allosteric product binding site' /> | <applet load='2v0n' scene='User:Tilman_Schirmer/Sandbox_201/5gp/1' size='300' frame='true' align='right' caption='Allosteric product binding site' /> | ||
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<applet load='1w25' scene='User:Tilman_Schirmer/Sandbox_201/Loose_dimer/3' size='250' frame='true' align='left' caption='non-activated (1w25)' /> <applet load='2v0n' scene='User:Tilman_Schirmer/Sandbox_201/Tight_dimer/2' size='250' frame='true' align='center' caption='activated (BeF3- modified; 2v0n)' /> | <applet load='1w25' scene='User:Tilman_Schirmer/Sandbox_201/Loose_dimer/3' size='250' frame='true' align='left' caption='non-activated (1w25)' /> <applet load='2v0n' scene='User:Tilman_Schirmer/Sandbox_201/Tight_dimer/2' size='250' frame='true' align='center' caption='activated (BeF3- modified; 2v0n)' /> | ||
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| - | == Non-activated conformation == | ||
| - | |||
| - | [[1w25]] | ||
| - | <applet load='1w25' scene='User:Tilman_Schirmer/Sandbox_201/Protomer/2' size='300' frame='true' align='right' caption='1w25' /> | ||
| - | |||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer/2'>Protomer</scene>: <scene name='User:Tilman_Schirmer/Sandbox_201/Rec/1'>Rec domain</scene>, | ||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Rec2/1'>Rec' domain</scene>, <scene name='User:Tilman_Schirmer/Sandbox_201/Ggdef/1'>GGDEF domain</scene> | ||
| - | |||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Loose_dimer/2'>Loose dimer</scene> | ||
| - | |||
| - | |||
| - | <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> | ||
| - | |||
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| - | == Activated conformation == | ||
| - | |||
| - | [[2v0n]] | ||
| - | |||
| - | <applet load='2v0n' scene='User:Tilman_Schirmer/Sandbox_201/Protomer_activeated/1' size='300' frame='true' align='right' caption='2v0n' /> | ||
| - | |||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer_activeated/1'>Protomer</scene> | ||
| - | |||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/Tight_dimer/3'>Tight dimer</scene> | ||
| - | |||
| - | |||
| - | <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> | ||
Current revision
PleD
Contents |
Overview
|
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
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The motif is part of the as identified in the structure of PleD in complex with . The GGDEFY domain binds only one GTP subsrate molecule. For the reaction to proceed, two GTP loaded GGDEF domains have to align antiparallely. MODEL.
Allosteric product binding site
|
C-di-GMP
Primary inhibition site (Ip)
Secondary inhibition site (Is)
Primary and secondary inhibition sites
Two conformations
non-activated (1w25)
activated (BeF3- modified; 2v0n)
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|
