5F29

Structure of RCK domain with cda


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.821 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • DOI: 10.1021/acs.biochem.5b00633
  • Primary Citation of Related Structures:  

  • 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 ...

    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

    †National Chung Hsing University Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, ROC.,‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC.,⊥Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, U.K.,§School of Biological Sciences, Nanyang Technological University, Singapore 637551.,∥School of Microbiology, Biosciences Institute, University College Cork, Cork, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Na+/H+ antiporter-like protein
A, B
73Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Find proteins for Q2FZQ4 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZQ4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2BA
Query on 2BA

Download SDF File 
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
bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate
C20 H24 N10 O12 P2
PDXMFTWFFKBFIN-XPWFQUROSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.821 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.489α = 90.00
b = 47.297β = 90.00
c = 70.174γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-12-01 
  • Released Date: 2017-02-01 
  • Deposition Author(s): Chin, K.H.

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2018-08-08
    Type: Data collection, Database references