7TGL

Crystal structure of AMP+PPi bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD.

Yang, J.Banas, V.S.Patel, K.D.Rivera, G.S.M.Mydy, L.S.Gulick, A.M.Wencewicz, T.A.

(2022) J Biol Chem 298: 102166-102166

  • DOI: 10.1016/j.jbc.2022.102166
  • Primary Citation of Related Structures:  
    7TGJ, 7TGK, 7TGL, 7TGM, 7TGN

  • PubMed Abstract: 
  • Siderophores are conditionally essential metabolites used by microbes for environmental iron sequestration. Most Streptomyces strains produce hydroxamate-based desferrioxamine (DFO) siderophores composed of repeating units of N 1 -hydroxy-cadaverine (or N 1 -hydroxy-putrescine) and succinate ...

    Siderophores are conditionally essential metabolites used by microbes for environmental iron sequestration. Most Streptomyces strains produce hydroxamate-based desferrioxamine (DFO) siderophores composed of repeating units of N 1 -hydroxy-cadaverine (or N 1 -hydroxy-putrescine) and succinate. The DFO biosynthetic operon, desABCD, is highly conserved in Streptomyces; however, expression of desABCD alone does not account for the vast structural diversity within this natural product class. Here, we report the in vitro reconstitution and biochemical characterization of four DesD orthologs from Streptomyces strains that produce unique DFO siderophores. Under in vitro conditions, all four DesD orthologs displayed similar saturation steady-state kinetics (V max  = 0.9-2.5 μM⋅min -1 ) and produced the macrocyclic trimer DFOE as the favored product, suggesting a conserved role for DesD in the biosynthesis of DFO siderophores. We further synthesized a structural mimic of N 1 -hydroxy-N 1 -succinyl-cadaverine (HSC)-acyl-adenylate, the HSC-acyl sulfamoyl adenosine analog (HSC-AMS), and obtained crystal structures of DesD in the ATP-bound, AMP/PP i -bound, and HSC-AMS/P i -bound forms. We found HSC-AMS inhibited DesD orthologs (IC 50 values = 48-53 μM) leading to accumulation of linear trimeric DFOG and di-HSC at the expense of macrocyclic DFOE. Addition of exogenous PP i enhanced DesD inhibition by HSC-AMS, presumably via stabilization of the DesD-HSC-AMS complex, similar to the proposed mode of adenylate stabilization where PP i remains buried in the active site. In conclusion, our data suggest that acyl-AMS derivatives may have utility as chemical probes and bisubstrate inhibitors to reveal valuable mechanistic and structural insight for this unique family of adenylating enzymes.


    Organizational Affiliation

    Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA. Electronic address: wencewicz@wustl.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Desferrioxamine synthetase DesDA, B, C, D, E612Streptomyces griseoflavusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
BA [auth C],
HA [auth D],
I [auth A],
RA [auth E],
S [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
PPV (Subject of Investigation/LOI)
Query on PPV

Download Ideal Coordinates CCD File 
AA [auth C],
GA [auth D],
H [auth A],
QA [auth E],
R [auth B]
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
IA [auth D],
J [auth A],
JA [auth D],
KA [auth D],
SA [auth E],
IA [auth D],
J [auth A],
JA [auth D],
KA [auth D],
SA [auth E],
T [auth B],
U [auth B],
V [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
M [auth B],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
M [auth B],
N [auth B],
NA [auth E],
O [auth B],
OA [auth E],
P [auth B],
PA [auth E],
Q [auth B],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth C],
DA [auth C],
K [auth A],
L [auth A],
LA [auth D],
CA [auth C],
DA [auth C],
K [auth A],
L [auth A],
LA [auth D],
MA [auth D],
TA [auth E],
UA [auth E],
W [auth B],
X [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.501α = 90
b = 236.745β = 90
c = 330.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM136235
National Science Foundation (NSF, United States)United States1654611

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references