6HVM

Structural characterization of CdaA-APO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of the c-di-AMP-synthesizing enzyme CdaA.

Heidemann, J.L.Neumann, P.Dickmanns, A.Ficner, R.

(2019) J.Biol.Chem. 294: 10463-10470

  • DOI: 10.1074/jbc.RA119.009246
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cyclic di-AMP (c-di-AMP) is the only second messenger known to be essential for bacterial growth. It has been mainly found in gram-positive bacteria, including pathogenic bacteria like <i>Listeria monocytogenes. </i> CdaA is the sole di-adenylate cy ...

    Cyclic di-AMP (c-di-AMP) is the only second messenger known to be essential for bacterial growth. It has been mainly found in gram-positive bacteria, including pathogenic bacteria like Listeria monocytogenes. CdaA is the sole di-adenylate cyclase in L. monocytogenes rendering this enzyme an attractive target for the development of novel antibiotic compounds. Here we report crystal structures of CdaA from L. monocytogenes in the apo-state, in the post-catalytic state with bound c-di-AMP and catalytic Co2+ ions, as well as in a complex with AMP. These structures reveal the flexibility of a tyrosine side-chain involved in locking the adenine ring after ATP binding. The essential role of this tyrosine was confirmed by mutation to Ala leading to a drastic loss of enzymatic activity.


    Organizational Affiliation

    University Goettingen, Germany.,Molecular Structural Biology, University of Goettingen, Germany.,University of Goettingen, Germany.,University of Goettingen.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diadenylate cyclase
A, B
178Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)Mutation(s): 0 
Gene Names: dacA (cdaA)
EC: 2.7.7.85
Find proteins for Q8Y5E4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Go to UniProtKB:  Q8Y5E4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
B
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.486α = 90.00
b = 64.896β = 90.00
c = 129.809γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Germany--

Revision History 

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Database references