4YP1

Misting with CDA

DOI: 10.2210/pdb4YP1/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-03-12 Released: 2015-10-07
Deposition Author(s): Chin, K.H., Chen, C.K., Tu, Z.I., Chou, S.H.
Funding Organization(s): Ministry of Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.260
R-Value Work: 0.210
R-Value Observed: 0.210

wwPDB Validation3D Report Full Report

Literature

Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK.

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.

(2015) Biochemistry 54: 4936-4951

PubMed: 26171638 Search on PubMed
DOI: 10.1021/acs.biochem.5b00633
Structures With Same Primary Citation

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.

Organizational Affiliation:

‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Stimulator of interferon genes protein	A, B	210	Mus musculus	Mutation(s): 0 Gene Names: Tmem173, Eris Mita, Mpys, Sting, Sting1, Eris, Mita
Find proteins for Q3TBT3 (Mus musculus) Go to UniProtKB: Q3TBT3
NIH Common Fund Data Resources
IMPC MGI:1919762
Protein Feature View Full Protein Feature View for Q3TBT3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2BA Query on 2BA Download CCD File	A	(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 C₂₀ H₂₄ N₁₀ O₁₂ P₂ PDXMFTWFFKBFIN-XPWFQUROSA-N		Ligand Interaction