6HVL

CdaA complex with c-di-AMP and AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.2 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:  
    6HVL, 6HVN, 6HVM

  • PubMed Abstract: 
  • Cyclic di-AMP (c-di-AMP) is the only second messenger known to be essential for bacterial growth. It has been found mainly in Gram-positive bacteria, including pathogenic bacteria like Listeria monocytogenes CdaA is the sole diadenylate cyclase in L ...

    Cyclic di-AMP (c-di-AMP) is the only second messenger known to be essential for bacterial growth. It has been found mainly in Gram-positive bacteria, including pathogenic bacteria like Listeria monocytogenes CdaA is the sole diadenylate cyclase in L. monocytogenes , making 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 Co 2+ 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 drastic loss of enzymatic activity.


    Organizational Affiliation

    From the Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077 Göttingen, Germany rficner@uni-goettingen.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Diadenylate cyclaseA, B178Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: dacAcdaAlmo2120
EC: 2.7.7.85
UniProt
Find proteins for Q8Y5E4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y5E4 
Go to UniProtKB:  Q8Y5E4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2BA (Subject of Investigation/LOI)
Query on 2BA

Download Ideal Coordinates CCD File 
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
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
F [auth B]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
D [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.9α = 90
b = 121.9β = 90
c = 141.16γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Derived calculations