5F29

Structure of RCK domain with cda

Summary for 5F29

• Entry DOI: 10.2210/pdb5f29/pdb
• Related: 4YS2
• Descriptor: Na+/H+ antiporter-like protein, (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 (3 entities in total)
• Functional Keywords: rck domain, cda, cpaa, transport protein
• Biological source: Staphylococcus aureus
• Total number of polymer chains: 2
• Total formula weight: 18241.96

Authors

Chin, K.H. (deposition date: 2015-12-01, release date: 2017-02-01, Last modification date: 2024-11-20)

Primary citation

Chin, K.H.,Liang, J.M.,Yang, J.G.,Shih, M.S.,Tu, Z.L.,Wang, Y.C.,Sun, X.H.,Hu, N.J.,Liang, Z.X.,Dow, J.M.,Ryan, R.P.,Chou, S.H.
Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK.
Biochemistry, 54:4936-4951, 2015

PubMed Abstract: 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 Å. This structure revealed two well-liganded water molecules, each interacting with one of the adenine bases by a unique H2Olp-π 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-π, cation-π, backbone-π, or H2Olp-π interaction, but more commonly in the outer interaction zone by hydrophobic CH-π or π-π 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.

PubMed: 26171638
DOI: 10.1021/acs.biochem.5b00633

Experimental method

X-RAY DIFFRACTION (1.821 Å)