4NE0

Crystal structure of non-heme iron oxygenase OrfP D157A mutant in complex with (3S)-hydroxy-L-Arg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report



Literature

Biosynthesis of streptolidine involved two unexpected intermediates produced by a dihydroxylase and a cyclase through unusual mechanisms

Chang, C.Y.Lyu, S.Y.Liu, Y.C.Hsu, N.S.Wu, C.C.Tang, C.F.Lin, K.H.Ho, J.Y.Wu, C.J.Tsai, M.D.Li, T.L.

(2014) Angew Chem Int Ed Engl 53: 1943-1948

  • DOI: 10.1002/anie.201307989
  • Primary Citation of Related Structures:  
    4M23, 4M25, 4M26, 4M27, 4M2I, 4M2J, 4M2K, 4M2M, 4M2C, 4M2E

  • PubMed Abstract: 
  • Streptothricin-F (STT-F), one of the early-discovered antibiotics, consists of three components, a β-lysine homopolymer, an aminosugar D-gulosamine, and an unusual bicyclic streptolidine. The biosynthesis of streptolidine is a long-lasting but unreso ...

    Streptothricin-F (STT-F), one of the early-discovered antibiotics, consists of three components, a β-lysine homopolymer, an aminosugar D-gulosamine, and an unusual bicyclic streptolidine. The biosynthesis of streptolidine is a long-lasting but unresolved puzzle. Herein, a combination of genetic/biochemical/structural approaches was used to unravel this problem. The STT gene cluster was first sequenced from a Streptomyces variant BCRC 12163, wherein two gene products OrfP and OrfR were characterized in vitro to be a dihydroxylase and a cyclase, respectively. Thirteen high-resolution crystal structures for both enzymes in different reaction intermediate states were snapshotted to help elucidate their catalytic mechanisms. OrfP catalyzes an Fe(II) -dependent double hydroxylation reaction converting L-Arg into (3R,4R)-(OH)2 -L-Arg via (3S)-OH-L-Arg, while OrfR catalyzes an unusual PLP-dependent elimination/addition reaction cyclizing (3R,4R)-(OH)2 -L-Arg to the six-membered (4R)-OH-capreomycidine. The biosynthetic mystery finally comes to light as the latter product was incorporation into STT-F by a feeding experiment.


    Organizational Affiliation

    Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115 (Taiwan).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-arginine beta-hydroxylaseABCD364Streptomyces lavendulae subsp. lavendulaeMutation(s): 1 
Gene Names: vioCSLAV_37395
EC: 1.14.11.41
Find proteins for G9MBV2 (Streptomyces lavendulae subsp. lavendulae)
Explore G9MBV2 
Go to UniProtKB:  G9MBV2
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZZU
Query on ZZU

Download CCD File 
C, D
(2S,3S)-3-HYDROXYARGININE
C6 H14 N4 O3
VIDUVSPOWYVZIC-IMJSIDKUSA-N
 Ligand Interaction
SIN
Query on SIN

Download CCD File 
C, D
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.861α = 90
b = 117.33β = 91.33
c = 95.815γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release