C-di-GMP specific phosphodiesterases
From Proteopedia
(Difference between revisions)
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| - | [[C-di-GMP signaling| | + | <StructureSection load='2w27' size='450' side='right' scene='' caption=''> |
| + | [[C-di-GMP signaling|Back to C-di-GMP signaling]] | ||
== YukI == | == YukI == | ||
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| - | <applet load='2w27.pdb' scene='User:Tilman_Schirmer/Sandbox_202/Yuki_dimer/3' size='300' frame='true' align='right' caption='YukI [[2w27]]' /> | ||
<scene name='User:Tilman_Schirmer/Sandbox_202/Yuki_dimer/3'>YukI</scene> is a dimer with each protomer composed of an <scene name='User:Tilman_Schirmer/Sandbox_202/Eal_domain/1'>EAL domain</scene> (with TIM barrel fold), a long <scene name='User:Tilman_Schirmer/Sandbox_202/Connection/1'>helical linker</scene>, and a <scene name='User:Tilman_Schirmer/Sandbox_202/Pas_like_domain/1'>PAS-like domain</scene>. <br> | <scene name='User:Tilman_Schirmer/Sandbox_202/Yuki_dimer/3'>YukI</scene> is a dimer with each protomer composed of an <scene name='User:Tilman_Schirmer/Sandbox_202/Eal_domain/1'>EAL domain</scene> (with TIM barrel fold), a long <scene name='User:Tilman_Schirmer/Sandbox_202/Connection/1'>helical linker</scene>, and a <scene name='User:Tilman_Schirmer/Sandbox_202/Pas_like_domain/1'>PAS-like domain</scene>. <br> | ||
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The <scene name='User:Tilman_Schirmer/Sandbox_202/Active_site_ligand/3'>c-di-GMP substrate</scene> is bound flat upon the actve site with the divalent metal (here Ca<sup>++</sup>) being sandwiched between binding site and c-di-GMP. | The <scene name='User:Tilman_Schirmer/Sandbox_202/Active_site_ligand/3'>c-di-GMP substrate</scene> is bound flat upon the actve site with the divalent metal (here Ca<sup>++</sup>) being sandwiched between binding site and c-di-GMP. | ||
| - | + | == BlrP1 == | |
| - | < | + | <scene name='User:Tilman_Schirmer/Sandbox_202/Blrp1_dimer/3'>BlrP1</scene> ([[3gg0]]) |
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<scene name='User:Tilman_Schirmer/Sandbox_202/Blrp1_dimer/2'>BlrP1</scene> | <scene name='User:Tilman_Schirmer/Sandbox_202/Blrp1_dimer/2'>BlrP1</scene> | ||
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<scene name='User:Tilman_Schirmer/Sandbox_202/Blrp1_active_site_ligand_hoh/2'>Active site + ligand + Mn + HOH</scene> | <scene name='User:Tilman_Schirmer/Sandbox_202/Blrp1_active_site_ligand_hoh/2'>Active site + ligand + Mn + HOH</scene> | ||
| - | < | + | </StructureSection> |
| - | + | __NOTOC__ | |
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==3D structure of YukI== | ==3D structure of YukI== | ||
Revision as of 11:31, 27 August 2013
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3D structure of YukI
Updated on 27-August-2013
2bas – BsYkuI – Bacillus subtilis
2w27 – BsYkuI + C-di-GMP
3D structure of BlrP1
3gfx, 3gfy, 3gfz, 3gg0, 3gg1 – KpBlrP1 + C-di-GMP - Klebsiella pneumoniae
2kb2 - KpBlrP1 BLUF domain - NMR
3D structures of phosphodiesterase
References
YkuI structure 2w27:
- Minasov G, Padavattan S, Shuvalova L, Brunzelle JS, Miller DJ, Basle A, Massa C, Collart FR, Schirmer T, Anderson WF. Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains. J Biol Chem. 2009 May 8;284(19):13174-84. Epub 2009 Feb 24. PMID:19244251 doi:10.1074/jbc.M808221200
BlrP1 structure 3gg0:
- Barends TR, Hartmann E, Griese JJ, Beitlich T, Kirienko NV, Ryjenkov DA, Reinstein J, Shoeman RL, Gomelsky M, Schlichting I. Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature. 2009 Jun 18;459(7249):1015-8. PMID:19536266 doi:10.1038/nature07966
Proteopedia Page Contributors and Editors (what is this?)
Michal Harel, Joel L. Sussman, Alexander Berchansky, Tilman Schirmer
