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| | ==HADDOCK structure of GtYybT PAS Homodimer== | | ==HADDOCK structure of GtYybT PAS Homodimer== |
| - | <StructureSection load='2m1c' size='340' side='right' caption='[[2m1c]], [[NMR_Ensembles_of_Models | 4 NMR models]]' scene=''> | + | <StructureSection load='2m1c' size='340' side='right'caption='[[2m1c]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2m1c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_ng80-2 Geobacillus thermodenitrificans ng80-2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2M1C FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2m1c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_NG80-2 Geobacillus thermodenitrificans NG80-2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M1C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M1C FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DHH subfamily 1, GTNG_3419 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=420246 Geobacillus thermodenitrificans NG80-2])</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2m1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m1c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2m1c RCSB], [http://www.ebi.ac.uk/pdbsum/2m1c PDBsum]</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=2m1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m1c OCA], [https://pdbe.org/2m1c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m1c RCSB], [https://www.ebi.ac.uk/pdbsum/2m1c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m1c ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/GDPP_GEOTN GDPP_GEOTN] Has phosphodiesterase (PDE) activity against cyclic-di-AMP (c-di-AMP) and to a much lesser extent against cyclic-di-GMP (c-di-GMP) in the DHH/DHHA1 domains. Also has ATPase activity, probably via the GGDEF domain. May monitor cellular heme or NO levels.[UniProtKB:P37484] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 2m1c" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Geobacillus thermodenitrificans ng80-2]] | + | [[Category: Geobacillus thermodenitrificans NG80-2]] |
| - | [[Category: Lescar, J]] | + | [[Category: Large Structures]] |
| - | [[Category: Liang, Z X]] | + | [[Category: Lescar J]] |
| - | [[Category: Pasunooti, S]] | + | [[Category: Liang ZX]] |
| - | [[Category: Pervushin, K]] | + | [[Category: Pasunooti S]] |
| - | [[Category: Rao, F]] | + | [[Category: Pervushin K]] |
| - | [[Category: Soehano, I]] | + | [[Category: Rao F]] |
| - | [[Category: Tan, E]] | + | [[Category: Soehano I]] |
| - | [[Category: Hydrolase]]
| + | [[Category: Tan E]] |
| - | [[Category: Ligand binding]]
| + | |
| - | [[Category: Pas domain]]
| + | |
| - | [[Category: Yybt]]
| + | |
| Structural highlights
Function
GDPP_GEOTN Has phosphodiesterase (PDE) activity against cyclic-di-AMP (c-di-AMP) and to a much lesser extent against cyclic-di-GMP (c-di-GMP) in the DHH/DHHA1 domains. Also has ATPase activity, probably via the GGDEF domain. May monitor cellular heme or NO levels.[UniProtKB:P37484]
Publication Abstract from PubMed
The Bacillus subtilis protein YybT (or GdpP) and its homologs were recently established as stress signaling proteins that exert their biological effect by degrading the bacterial messenger c-di-AMP. YybT homologs contain a small Per-ARNT-Sim (PAS) domain (ca. 80 amino acids) that can bind b-type heme with 1:1 stoichiometry despite the small size of the domain and the lack of a conserved heme iron-coordinating residue. We determined the solution structure of the PAS domain of GtYybT from Geobacillus thermodenitrificans by NMR spectroscopy to further probe its function. The solution structure confirms that PASGtYybT adopts the characteristic PAS fold composed of a five-stranded antiparallel beta sheet and a few short alpha-helices. One alpha-helix and three central beta-strands of PASGtYybT are noticeably shorter than those of the typical PAS domains. Despite the small size of the protein domain, a hydrophobic pocket is formed by the side chains of non-polar residues stemming from the beta-strands and alpha-helices. A set of residues in the vicinity of the pocket and in the C-terminal region at the dimeric interface exhibit perturbed NMR parameters in the presence of heme or zinc protoporphyrin. Together, the results unveil a compact PAS domain with a potential ligand-binding pocket and reinforce the view that the PASYybT domains function as regulatory domains in the modulation of cellular c-di-AMP concentration.
Solution Structure of the PAS Domain of a Thermophilic YybT Homolog Reveals a Potential Ligand-Binding Site.,Tan E, Rao F, Pasunooti S, Pham TH, Soehano I, Turner MS, Liew CW, Lescar J, Pervushin K, Liang ZX J Biol Chem. 2013 Mar 15. PMID:23504327[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tan E, Rao F, Pasunooti S, Pham TH, Soehano I, Turner MS, Liew CW, Lescar J, Pervushin K, Liang ZX. Solution Structure of the PAS Domain of a Thermophilic YybT Homolog Reveals a Potential Ligand-Binding Site. J Biol Chem. 2013 Mar 15. PMID:23504327 doi:10.1074/jbc.M112.437764
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