5f29: Difference between revisions
New page: '''Unreleased structure''' The entry 5f29 is ON HOLD Authors: Chin, K. Description: RCK domain with cda Category: Unreleased Structures Category: Chin, K |
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==Structure of RCK domain with cda== | |||
<StructureSection load='5f29' size='340' side='right'caption='[[5f29]], [[Resolution|resolution]] 1.82Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5f29]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F29 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.821Å</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5f29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f29 OCA], [https://pdbe.org/5f29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f29 RCSB], [https://www.ebi.ac.uk/pdbsum/5f29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f29 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Cyclic di-AMP (c-di-AMP) is a relatively new member of the family of bacterial cyclic dinucleotide second messengers. It has attracted significant attention in recent years because of the abundant roles it plays in a variety of Gram-positive bacteria. The structural features that allow diverse bacterial proteins to bind c-di-AMP are not fully understood. Here we report the biophysical and structural studies of c-di-AMP in complex with a bacterial cation-proton antiporter (CpaA) RCK (regulator of the conductance of K(+)) protein from Staphylococcus aureus (Sa). The crystal structure of the SaCpaA_RCK C-terminal domain (CTD) in complex with c-di-AMP was determined to a resolution of 1.81 A. This structure revealed two well-liganded water molecules, each interacting with one of the adenine bases by a unique H2Olp-pi interaction to stabilize the complex. Sequence blasting using the SaCpaA_RCK primary sequence against the bacterial genome database returned many CpaA analogues, and alignment of these sequences revealed that the active site residues are all well-conserved, indicating a universal c-di-AMP binding mode for CpaA_RCK. A proteoliposome activity assay using the full-length SaCpaA membrane protein indicated that c-di-AMP binding alters its antiporter activity by approximately 40%. A comparison of this structure to all other reported c-di-AMP-receptor complex structures revealed that c-di-AMP binds to receptors in either a "U-shape" or "V-shape" mode. The two adenine rings are stabilized in the inner interaction zone by a variety of CH-pi, cation-pi, backbone-pi, or H2Olp-pi interaction, but more commonly in the outer interaction zone by hydrophobic CH-pi or pi-pi interaction. The structures determined to date provide an understanding of the mechanisms by which a single c-di-AMP can interact with a variety of receptor proteins, and how c-di-AMP binds receptor proteins in a special way different from that of c-di-GMP. | |||
Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK.,Chin KH, Liang JM, Yang JG, Shih MS, Tu ZL, Wang YC, Sun XH, Hu NJ, Liang ZX, Dow JM, Ryan RP, Chou SH Biochemistry. 2015 Aug 11;54(31):4936-51. doi: 10.1021/acs.biochem.5b00633. Epub , 2015 Jul 27. PMID:26171638<ref>PMID:26171638</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Chin | <div class="pdbe-citations 5f29" style="background-color:#fffaf0;"></div> | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Staphylococcus aureus]] | |||
[[Category: Chin KH]] | |||
Latest revision as of 07:03, 21 November 2024
Structure of RCK domain with cdaStructure of RCK domain with cda
Structural highlights
Publication Abstract from PubMedCyclic di-AMP (c-di-AMP) is a relatively new member of the family of bacterial cyclic dinucleotide second messengers. It has attracted significant attention in recent years because of the abundant roles it plays in a variety of Gram-positive bacteria. The structural features that allow diverse bacterial proteins to bind c-di-AMP are not fully understood. Here we report the biophysical and structural studies of c-di-AMP in complex with a bacterial cation-proton antiporter (CpaA) RCK (regulator of the conductance of K(+)) protein from Staphylococcus aureus (Sa). The crystal structure of the SaCpaA_RCK C-terminal domain (CTD) in complex with c-di-AMP was determined to a resolution of 1.81 A. This structure revealed two well-liganded water molecules, each interacting with one of the adenine bases by a unique H2Olp-pi interaction to stabilize the complex. Sequence blasting using the SaCpaA_RCK primary sequence against the bacterial genome database returned many CpaA analogues, and alignment of these sequences revealed that the active site residues are all well-conserved, indicating a universal c-di-AMP binding mode for CpaA_RCK. A proteoliposome activity assay using the full-length SaCpaA membrane protein indicated that c-di-AMP binding alters its antiporter activity by approximately 40%. A comparison of this structure to all other reported c-di-AMP-receptor complex structures revealed that c-di-AMP binds to receptors in either a "U-shape" or "V-shape" mode. The two adenine rings are stabilized in the inner interaction zone by a variety of CH-pi, cation-pi, backbone-pi, or H2Olp-pi interaction, but more commonly in the outer interaction zone by hydrophobic CH-pi or pi-pi interaction. The structures determined to date provide an understanding of the mechanisms by which a single c-di-AMP can interact with a variety of receptor proteins, and how c-di-AMP binds receptor proteins in a special way different from that of c-di-GMP. Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK.,Chin KH, Liang JM, Yang JG, Shih MS, Tu ZL, Wang YC, Sun XH, Hu NJ, Liang ZX, Dow JM, Ryan RP, Chou SH Biochemistry. 2015 Aug 11;54(31):4936-51. doi: 10.1021/acs.biochem.5b00633. Epub , 2015 Jul 27. PMID:26171638[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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