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| | ==Crystal structure of VCA0042 (L135R) complexed with c-di-GMP== | | ==Crystal structure of VCA0042 (L135R) complexed with c-di-GMP== |
| - | <StructureSection load='3kyg' size='340' side='right' caption='[[3kyg]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3kyg' size='340' side='right'caption='[[3kyg]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3kyg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KYG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3kyg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KYG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VC_A0042 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyg OCA], [http://pdbe.org/3kyg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kyg RCSB], [http://www.ebi.ac.uk/pdbsum/3kyg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kyg ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyg OCA], [https://pdbe.org/3kyg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kyg RCSB], [https://www.ebi.ac.uk/pdbsum/3kyg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kyg ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/YCGRL_VIBCH YCGRL_VIBCH]] May act as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. Increasing levels of c-di-GMP lead to decreased motility (Potential). Binds bis-(3'-5') cyclic diguanylic acid (c-di-GMP) with a dissociation constant of 170 nM in the presence of 10 mM KCl and with 100 nM in its absence. Binds 1 to 2 c-di-GMP per subunit. Only 1 c-di-GMP is seen in the wild-type crystal, while 2 are seen in the mutant. Depending on the concentration of K(+) stoichiometries of 1:1, 1.43:1 and 2:1 are determined by isothermal titration calorimetry. | + | [https://www.uniprot.org/uniprot/YCGRL_VIBCH YCGRL_VIBCH] May act as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. Increasing levels of c-di-GMP lead to decreased motility (Potential). Binds bis-(3'-5') cyclic diguanylic acid (c-di-GMP) with a dissociation constant of 170 nM in the presence of 10 mM KCl and with 100 nM in its absence. Binds 1 to 2 c-di-GMP per subunit. Only 1 c-di-GMP is seen in the wild-type crystal, while 2 are seen in the mutant. Depending on the concentration of K(+) stoichiometries of 1:1, 1.43:1 and 2:1 are determined by isothermal titration calorimetry. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillo virgola del koch trevisan 1884]] | + | [[Category: Large Structures]] |
| - | [[Category: Choi, B S]] | + | [[Category: Vibrio cholerae]] |
| - | [[Category: Kim, H]] | + | [[Category: Choi BS]] |
| - | [[Category: Ko, J]] | + | [[Category: Kim H]] |
| - | [[Category: Ryu, K S]] | + | [[Category: Ko J]] |
| - | [[Category: C-di-gmp]] | + | [[Category: Ryu KS]] |
| - | [[Category: Pilz domain]]
| + | |
| - | [[Category: Pp4397]]
| + | |
| - | [[Category: Unknown function]]
| + | |
| - | [[Category: Vca0042]]
| + | |
| Structural highlights
Function
YCGRL_VIBCH May act as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. Increasing levels of c-di-GMP lead to decreased motility (Potential). Binds bis-(3'-5') cyclic diguanylic acid (c-di-GMP) with a dissociation constant of 170 nM in the presence of 10 mM KCl and with 100 nM in its absence. Binds 1 to 2 c-di-GMP per subunit. Only 1 c-di-GMP is seen in the wild-type crystal, while 2 are seen in the mutant. Depending on the concentration of K(+) stoichiometries of 1:1, 1.43:1 and 2:1 are determined by isothermal titration calorimetry.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Cyclic diguanylate (c-di-GMP) is a global regulator that modulates pathogen virulence and biofilm formation in bacteria. Although a bioinformatic study revealed that PilZ domain proteins are the long-sought c-di-GMP binding proteins, the mechanism by which c-di-GMP regulates them is uncertain. Pseudomonas putida PP4397 is one such protein that contains YcgR-N and PilZ domains and the apo-PP4397 structure was solved earlier by the Joint Center for Structural Genomics. We determined the crystal structure of holo-PP4397 and found that two intercalated c-di-GMPs fit into the junction of its YcgR-N and PilZ domains. Moreover, c-di-GMP binding induces PP4397 to undergo a dimer-to-monomer transition. Interestingly, another PilZ domain protein, VCA0042, binds to a single molecule of c-di-GMP, and both its apo and holo forms are dimeric. Mutational studies and the additional crystal structure of holo-VCA0042 (L135R) showed that the Arg122 residue of PP4397 is crucial for the recognition of two molecules of c-di-GMP. Thus, PilZ domain proteins exhibit different c-di-GMP binding stoichiometry and quaternary structure, and these differences are expected to play a role in generating diverse forms of c-di-GMP-mediated regulation.
Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by Pilz domain proteins.,Ko J, Ryu KS, Kim H, Shin JS, Lee JO, Cheong C, Choi BS J Mol Biol. 2010 Apr 23;398(1):97-110. Epub 2010 Mar 10. PMID:20226196[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ko J, Ryu KS, Kim H, Shin JS, Lee JO, Cheong C, Choi BS. Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by Pilz domain proteins. J Mol Biol. 2010 Apr 23;398(1):97-110. Epub 2010 Mar 10. PMID:20226196 doi:10.1016/j.jmb.2010.03.007
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