4YP1

Misting with CDA

PDB 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 Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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
Primary Citation of Related Structures:
4YP1, 5F29

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:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A, B	210	Mus musculus	Mutation(s): 0 Gene Names: Tmem173, Eris Mita, Mpys, Sting, Sting1, Eris, Mita
UniProt & NIH Common Fund Data Resources
Find proteins for Q3TBT3 (Mus musculus) Explore Q3TBT3 Go to UniProtKB: Q3TBT3
IMPC: MGI:1919762
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3TBT3
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2BA Query on 2BA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth 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