User:Tilman Schirmer/Sandbox 201
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| - | + | [[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)' /> | |
| - | ===1.2 Domain structure === | ||
| + | <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, | ||
| + | and a C-terminal <scene name='User:Tilman_Schirmer/Sandbox_201/Protomer_ggdef/1'>GGDEF</scene> domain that confers the catalytic acitvity. | ||
| - | + | [[Image:Pled_domains_1.jpg|left]] | |
| - | + | ||
| - | <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/ | + | 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. |
| - | <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> | ||
| - | ---- | ||
| - | === 1.4 Substrate binding site === | ||
| - | <applet load='2v0n' scene='User:Tilman_Schirmer/Sandbox_201/Substrate_binding_site/2' size='300' frame='true' align='right' caption='2v0n' /> | ||
| - | < | + | <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)' /> |
| - | ---- | ||
| - | = | + | 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. |
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| - | ==== C-di-GMP ==== | ||
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/5gp/1'>5GP</scene> | ||
| - | ---- | ||
| - | ==== Primary inhibition site (Ip) ==== | ||
| - | < | + | <br><br><br><br><br><br><br><br><br><br><br><br><br> |
| - | <scene | + | === 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' /> | ||
| - | ---- | ||
| - | === | + | === C-di-GMP === |
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/ | + | <scene name='User:Tilman_Schirmer/Sandbox_201/C-di-gmp_monomer/1'>C-di-GMP monomer</scene> |
| - | + | ||
| - | + | ||
| + | <scene name='User:Tilman_Schirmer/Sandbox_201/C-di-gmp_dimer/1'>C-di-GMP 'dimer'</scene> | ||
---- | ---- | ||
| - | + | === Primary inhibition site (Ip) === | |
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/ | + | <scene name='User:Tilman_Schirmer/Sandbox_201/Primary_inhibition_site/2'>Primary inhibition site</scene> |
| - | + | ||
| - | + | ||
| - | <br><br> | ||
---- | ---- | ||
| - | === | + | === Secondary inhibition site (Is) === |
| - | + | <scene name='User:Tilman_Schirmer/Sandbox_201/Secondary_inhibition_site/1'>Secondary inhibition site</scene> | |
| - | + | ||
| - | + | ||
| - | < | + | |
---- | ---- | ||
| - | === | + | === Primary and secondary inhibition sites === |
| - | + | <scene name='User:Tilman_Schirmer/Sandbox_201/Prim_sec_inhibition_site/1'>Primary and secondary inhibition sites</scene> | |
| - | < | + | |
| - | <scene name='User:Tilman_Schirmer/Sandbox_201/ | + | <scene name='User:Tilman_Schirmer/Sandbox_201/Prim_sec_inhibition_site_5gp/1'>Primary and secondary inhibition sites + 5GP</scene> |
| - | + | ||
| - | < | + | <br><br><br><br> |
| + | == Two conformations == | ||
| - | + | [[Image:1w25_small.png|frame|left|non-activated (1w25)]] [[Image:2v0n_small_smaller2.png|frame|center|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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| - | == | + | |
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
|
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)
|
|
