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7ji4
From Proteopedia
(Difference between revisions)
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==Universal stress protein (USP) domain of KdpD histidine kinase in complex with second messenger c-di-AMP== | ==Universal stress protein (USP) domain of KdpD histidine kinase in complex with second messenger c-di-AMP== | ||
| - | <StructureSection load='7ji4' size='340' side='right'caption='[[7ji4]]' scene=''> | + | <StructureSection load='7ji4' size='340' side='right'caption='[[7ji4]], [[Resolution|resolution]] 2.30Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JI4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7ji4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staar Staar]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JI4 FirstGlance]. <br> |
| - | </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=7ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ji4 OCA], [https://pdbe.org/7ji4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ji4 RCSB], [https://www.ebi.ac.uk/pdbsum/7ji4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ji4 ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene></td></tr> |
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">kdpD_1, ERS072840_01892, SAMEA1469884_01983, SAMEA1531680_02090, SAMEA1531701_02007, SAST44_02327, SAST45_02303 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=282458 STAAR])</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=7ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ji4 OCA], [https://pdbe.org/7ji4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ji4 RCSB], [https://www.ebi.ac.uk/pdbsum/7ji4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ji4 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The KdpDE two-component system (TCS) regulates potassium homeostasis and virulence in various bacterial species. The KdpD histidine kinases of this system contain a universal stress protein (USP) domain which binds to the second messenger cyclic-di-adenosine monophosphate (c-di-AMP) for regulating transcriptional output from this TCS in Firmicutes such as Staphylococcus aureus. However, the structural basis of c-di-AMP specificity within the KdpD-USP domain is not well understood. Here, we resolved a 2.3 A crystal structure of the Staphylococcus aureus KdpD-USP domain (USPSa) complexed with c-di-AMP. Binding affinity analyses of USPSa mutants targeting the observed USPSa:c-di-AMP structural interface enabled the identification of the sequence residues that are required for c-di-AMP specificity. Based on the conservation of these residues in other Firmicutes, we identified the binding motif - (A/G/C)XSXSX2N(Y/F), which allowed us to predict c-di-AMP binding in other KdpD histidine kinases. Furthermore, we found that the USPSa domain contains structural features distinct from the canonical standalone USPs that bind ATP as a preferred ligand. These features include inward-facing conformations of its beta1-alpha1 and beta4-alpha4 loops, a short alpha2 helix, the absence of a triphosphate-binding Walker motif, and a unique dual phospho-ligand binding mode. It is therefore likely that USPSa-like domains in KdpD histidine kinases represent a novel subfamily of the USPs. | ||
| + | |||
| + | Structural basis of KdpD histidine kinase binding to the second messenger c-di-AMP.,Dutta A, Batish M, Parashar V J Biol Chem. 2021 May 11:100771. doi: 10.1016/j.jbc.2021.100771. PMID:33989637<ref>PMID:33989637</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7ji4" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Dutta A]] | + | [[Category: Staar]] |
| - | [[Category: Parashar V]] | + | [[Category: Dutta, A]] |
| + | [[Category: Parashar, V]] | ||
| + | [[Category: Histidine kinase]] | ||
| + | [[Category: Second messenger]] | ||
| + | [[Category: Signaling protein]] | ||
| + | [[Category: Two component system]] | ||
| + | [[Category: Universal stress protein]] | ||
Revision as of 09:14, 21 July 2021
Universal stress protein (USP) domain of KdpD histidine kinase in complex with second messenger c-di-AMP
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