6DYR

C-terminal condensation domain of Ebony in complex with Carcinine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Drosophila melanogasternonribosomal peptide synthetase Ebony encodes an atypical condensation domain.

Izore, T.Tailhades, J.Hansen, M.H.Kaczmarski, J.A.Jackson, C.J.Cryle, M.J.

(2019) Proc. Natl. Acad. Sci. U.S.A. 116: 2913-2918

  • DOI: 10.1073/pnas.1811194116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The protein Ebony from <i>Drosophila melanogaster </i> plays a central role in the regulation of histamine and dopamine in various tissues through condensation of these amines with β-alanine. Ebony is a rare example of a nonribosomal peptide synthet ...

    The protein Ebony from Drosophila melanogaster plays a central role in the regulation of histamine and dopamine in various tissues through condensation of these amines with β-alanine. Ebony is a rare example of a nonribosomal peptide synthetase (NRPS) from a higher eukaryote and contains a C-terminal sequence that does not correspond to any previously characterized NRPS domain. We have structurally characterized this C-terminal domain and have discovered that it adopts the aryl-alkylamine- N -acetyl transferase (AANAT) fold, which is unprecedented in NRPS biology. Through analysis of ligand-bound structures, activity assays, and binding measurements, we have determined how this atypical condensation domain is able to provide selectivity for both the carrier protein-bound amino acid and the amine substrates, a situation that remains unclear for standard condensation domains identified to date from NRPS assembly lines. These results demonstrate that the C terminus of Ebony encodes a eukaryotic example of an alternative type of NRPS condensation domain; they also illustrate how the catalytic components of such assembly lines are significantly more diverse than a minimal set of conserved functional domains.


    Organizational Affiliation

    The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,EMBL Australia, Monash University, Clayton, VIC 3800, Australia.,The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; thierry.izore@monash.edu max.cryle@monash.edu.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.,Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ebony
A
223Drosophila melanogasterMutation(s): 0 
Gene Names: e
Find proteins for A4GK78 (Drosophila melanogaster)
Go to UniProtKB:  A4GK78
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HJD
Query on HJD

Download SDF File 
Download CCD File 
A
N-[2-(1H-imidazol-5-yl)ethyl]-beta-alaninamide
C8 H14 N4 O
ANRUJJLGVODXIK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.520α = 90.00
b = 56.050β = 112.91
c = 49.730γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXphasing
PHENIXrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1140619

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-13
    Type: Data collection, Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Database references
  • Version 1.3: 2020-01-08
    Type: Author supporting evidence