Structure of EAL Enzyme Bd1971 - cAMP and cyclic-di-GMP bound form

Experimental Data Snapshot

  • Resolution: 2.83 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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Nucleotide signaling pathway convergence in a cAMP-sensing bacterial c-di-GMP phosphodiesterase.

Cadby, I.T.Basford, S.M.Nottingham, R.Meek, R.Lowry, R.Lambert, C.Tridgett, M.Till, R.Ahmad, R.Fung, R.Hobley, L.Hughes, W.S.Moynihan, P.J.Sockett, R.E.Lovering, A.L.

(2019) EMBO J 38: e100772-e100772

  • DOI: https://doi.org/10.15252/embj.2018100772
  • Primary Citation of Related Structures:  
    6HQ2, 6HQ3, 6HQ4, 6HQ5, 6HQ7

  • PubMed Abstract: 

    Bacterial usage of the cyclic dinucleotide c-di-GMP is widespread, governing the transition between motile/sessile and unicellular/multicellular behaviors. There is limited information on c-di-GMP metabolism, particularly on regulatory mechanisms governing control of EAL c-di-GMP phosphodiesterases. Herein, we provide high-resolution structures for an EAL enzyme Bd1971, from the predatory bacterium Bdellovibrio bacteriovorus, which is controlled by a second signaling nucleotide, cAMP. The full-length cAMP-bound form reveals the sensory N-terminus to be a domain-swapped variant of the cNMP/CRP family, which in the cAMP-activated state holds the C-terminal EAL enzyme in a phosphodiesterase-active conformation. Using a truncation mutant, we trap both a half-occupied and inactive apo-form of the protein, demonstrating a series of conformational changes that alter juxtaposition of the sensory domains. We show that Bd1971 interacts with several GGDEF proteins (c-di-GMP producers), but mutants of Bd1971 do not share the discrete phenotypes of GGDEF mutants, instead having an elevated level of c-di-GMP, suggesting that the role of Bd1971 is to moderate these levels, allowing "action potentials" to be generated by each GGDEF protein to effect their specific functions.

  • Organizational Affiliation

    Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EAL Enzyme Bd1971
A, B
398Bdellovibrio bacteriovorus HD100Mutation(s): 0 
Gene Names: Bd1971
Find proteins for Q6MLN6 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100))
Explore Q6MLN6 
Go to UniProtKB:  Q6MLN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MLN6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C2E

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
C20 H24 N10 O14 P2
Query on CMP

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
C10 H12 N5 O6 P
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.83 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.857α = 90
b = 83.857β = 90
c = 138.454γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary