Crystal structure of Streptomyces sviceus SsDesB

Experimental Data Snapshot

  • Resolution: 2.86 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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Characterization of a broadly specific cadaverine N-hydroxylase involved in desferrioxamine B biosynthesis in Streptomyces sviceus.

Giddings, L.A.Lountos, G.T.Kim, K.W.Brockley, M.Needle, D.Cherry, S.Tropea, J.E.Waugh, D.S.

(2021) PLoS One 16: e0248385-e0248385

  • DOI: https://doi.org/10.1371/journal.pone.0248385
  • Primary Citation of Related Structures:  
    6XBB, 6XBC

  • PubMed Abstract: 

    N-hydroxylating flavin-dependent monooxygenases (FMOs) are involved in the biosynthesis of hydroxamate siderophores, playing a key role in microbial virulence. Herein, we report the first structural and kinetic characterization of a novel alkyl diamine N-hydroxylase DesB from Streptomyces sviceus (SsDesB). This enzyme catalyzes the first committed step in the biosynthesis of desferrioxamine B, a clinical drug used to treat iron overload disorders. X-ray crystal structures of the SsDesB holoenzyme with FAD and the ternary complex with bound NADP+ were solved at 2.86 Å and 2.37 Å resolution, respectively, providing a structural view of the active site environment. SsDesB crystallized as a tetramer and the structure of the individual protomers closely resembles the structures of homologous N-hydroxylating FMOs from Erwinia amylovora (DfoA), Pseudomonas aeruginosa (PvdA), and Aspergillus fumigatus (SidA). Using NADPH oxidation, oxygen consumption, and product formation assays, kinetic parameters were determined for various substrates with SsDesB. SsDesB exhibited typical saturation kinetics with substrate inhibition at high concentrations of NAD(P)H as well as cadaverine. The apparent kcat values for NADPH in steady-state NADPH oxidation and oxygen consumption assays were 0.28 ± 0.01 s-1 and 0.24 ± 0.01 s-1, respectively. However, in product formation assays used to measure the rate of N-hydroxylation, the apparent kcat for NADPH (0.034 ± 0.008 s-1) was almost 10-fold lower under saturating FAD and cadaverine concentrations, reflecting an uncoupled reaction, and the apparent NADPH KM was 33 ± 24 μM. Under saturating FAD and NADPH concentrations, the apparent kcat and KM for cadaverine in Csaky assays were 0.048 ± 0.004 s-1 and 19 ± 9 μM, respectively. SsDesB also N-hydroxylated putrescine, spermidine, and L-lysine substrates but not alkyl (di)amines that were branched or had fewer than four methylene units in an alkyl chain. These data demonstrate that SsDesB has wider substrate scope compared to other well-studied ornithine and lysine N-hydroxylases, making it an amenable biocatalyst for the production of desferrioxamine B, derivatives, and other N-substituted products.

  • Organizational Affiliation

    Department of Chemistry, Smith College, Northampton, MA, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H
425Streptomyces sviceus ATCC 29083Mutation(s): 0 
Gene Names: SSEG_08523
Find proteins for B5HNG5 (Streptomyces sviceus (strain ATCC 29083 / DSM 924 / JCM 4929 / NBRC 13980 / NCIMB 11184 / NRRL 5439 / UC 5370))
Explore B5HNG5 
Go to UniProtKB:  B5HNG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5HNG5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.86 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.046α = 90
b = 151.174β = 91.58
c = 141.401γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description