5O5C

The crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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Literature

A complete structural characterization of the desferrioxamine E biosynthetic pathway from the fire blight pathogen Erwinia amylovora.

Salomone-Stagni, M.Bartho, J.D.Polsinelli, I.Bellini, D.Walsh, M.A.Demitri, N.Benini, S.

(2018) J Struct Biol 202: 236-249

  • DOI: 10.1016/j.jsb.2018.02.002
  • Primary Citation of Related Structures:  
    5O5C, 5O7O, 5O8P, 5O8R

  • PubMed Abstract: 
  • The Gram-negative bacterium Erwinia amylovora is the etiological agent of fire blight, a devastating disease which affects Rosaceae such as apple, pear and quince. The siderophore desferrioxamine E plays an important role in bacterial pathogenesis by scavenging iron from the host ...

    The Gram-negative bacterium Erwinia amylovora is the etiological agent of fire blight, a devastating disease which affects Rosaceae such as apple, pear and quince. The siderophore desferrioxamine E plays an important role in bacterial pathogenesis by scavenging iron from the host. DfoJ, DfoA and DfoC are the enzymes responsible for desferrioxamine production starting from lysine. We have determined the crystal structures of each enzyme in the desferrioxamine E pathway and demonstrate that the biosynthesis involves the concerted action of DfoJ, followed by DfoA and lastly DfoC. These data provide the first crystal structures of a Group II pyridoxal-dependent lysine decarboxylase, a cadaverine monooxygenase and a desferrioxamine synthetase. DfoJ is a homodimer made up of three domains. Each monomer contributes to the completion of the active site, which is positioned at the dimer interface. DfoA is the first structure of a cadaverine monooxygenase. It forms homotetramers whose subunits are built by two domains: one for FAD and one for NADP + binding, the latter of which is formed by two subdomains. We propose a model for substrate binding and the role of residues 43-47 as gate keepers for FAD binding and the role of Arg97 in cofactors turnover. DfoC is the first structure of a desferrioxamine synthetase and the first of a multi-enzyme siderophore synthetase coupling an acyltransferase domain with a Non-Ribosomal Peptide Synthetase (NRPS)-Independent Siderophore domain (NIS).


    Organizational Affiliation

    Bioorganic Chemistry and Bio-Crystallography Laboratory (B(2)Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100 Bolzano, Italy. Electronic address: stefano.benini@unibz.it.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative decarboxylase involved in desferrioxamine biosynthesis
A, B, C, D, E, F
A, B, C, D, E, F
519Erwinia amylovora CFBP1430Mutation(s): 0 
Gene Names: dfoJEAMY_3238
EC: 4.1.1
UniProt
Find proteins for D4I245 (Erwinia amylovora (strain CFBP1430))
Explore D4I245 
Go to UniProtKB:  D4I245
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4I245
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
I [auth C],
J [auth D],
K [auth E],
G [auth A],
H [auth B],
I [auth C],
J [auth D],
K [auth E],
L [auth F]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 269.791α = 90
b = 269.791β = 90
c = 56.194γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Autonomous province of BolzanoItalyvirelunce and pathogenesys of Erwinia amylovora

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references