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7ji4

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Current revision (14:52, 6 March 2024) (edit) (undo)
 
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<StructureSection load='7ji4' size='340' side='right'caption='[[7ji4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='7ji4' size='340' side='right'caption='[[7ji4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<table><tr><td colspan='2'>[[7ji4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_MRSA252 Staphylococcus aureus subsp. aureus MRSA252]. 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>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<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>
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<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='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>
<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>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/KDPD_STAA8 KDPD_STAA8] Member of the two-component regulatory system KdpD/KdpE that regulates the transcription of a series of virulence factors through sensing external K(+) concentrations (PubMed:21422185, PubMed:26195599). Regulates also capsular polysaccharide production (PubMed:20498265). May function as a membrane-associated protein kinase that phosphorylates KdpE in response to environmental signals. In turn, KpdE functions as a transcriptional regulator by direct binding to promoter regions of target genes including spa, hla, aur and geh (PubMed:21422185).<ref>PMID:20498265</ref> <ref>PMID:21422185</ref> <ref>PMID:26195599</ref>
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 7ji4" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Staar]]
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[[Category: Staphylococcus aureus subsp. aureus MRSA252]]
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[[Category: Dutta, A]]
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[[Category: Dutta A]]
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[[Category: Parashar, V]]
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[[Category: Parashar V]]
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[[Category: Histidine kinase]]
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[[Category: Second messenger]]
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[[Category: Signaling protein]]
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[[Category: Two component system]]
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[[Category: Universal stress protein]]
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Current revision

Universal stress protein (USP) domain of KdpD histidine kinase in complex with second messenger c-di-AMP

PDB ID 7ji4

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