Structure of rifampicin monooxygenase

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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The Structure of the Antibiotic Deactivating, N-hydroxylating Rifampicin Monooxygenase.

Liu, L.K.Abdelwahab, H.Martin Del Campo, J.S.Mehra-Chaudhary, R.Sobrado, P.Tanner, J.J.

(2016) J Biol Chem 291: 21553-21562

  • DOI: https://doi.org/10.1074/jbc.M116.745315
  • Primary Citation of Related Structures:  
    5KOW, 5KOX

  • PubMed Abstract: 

    Rifampicin monooxygenase (RIFMO) catalyzes the N-hydroxylation of the natural product antibiotic rifampicin (RIF) to 2'-N-hydroxy-4-oxo-rifampicin, a metabolite with much lower antimicrobial activity. RIFMO shares moderate sequence similarity with well characterized flavoprotein monooxygenases, but the protein has not been isolated and characterized at the molecular level. Herein, we report crystal structures of RIFMO from Nocardia farcinica, the determination of the oligomeric state in solution with small angle x-ray scattering, and the spectrophotometric characterization of substrate binding. The structure identifies RIFMO as a class A flavoprotein monooxygenase and is similar in fold and quaternary structure to MtmOIV and OxyS, which are enzymes in the mithramycin and oxytetracycline biosynthetic pathways, respectively. RIFMO is distinguished from other class A flavoprotein monooxygenases by its unique middle domain, which is involved in binding RIF. Small angle x-ray scattering analysis shows that RIFMO dimerizes via the FAD-binding domain to form a bell-shaped homodimer in solution with a maximal dimension of 110 Å. RIF binding was monitored using absorbance at 525 nm to determine a dissociation constant of 13 μm Steady-state oxygen consumption assays show that NADPH efficiently reduces the FAD only when RIF is present, implying that RIF binds before NADPH in the catalytic scheme. The 1.8 Å resolution structure of RIFMO complexed with RIF represents the precatalytic conformation that occurs before formation of the ternary E-RIF-NADPH complex. The RIF naphthoquinone blocks access to the FAD N5 atom, implying that large conformational changes are required for NADPH to reduce the FAD. A model for these conformational changes is proposed.

  • Organizational Affiliation

    From the Departments of Biochemistry and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pentachlorophenol 4-monooxygenase476Nocardia farcinicaMutation(s): 0 
Gene Names: pcpB_1ERS450000_00511
Find proteins for Q5YTV5 (Nocardia farcinica (strain IFM 10152))
Explore Q5YTV5 
Go to UniProtKB:  Q5YTV5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YTV5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
C27 H33 N9 O15 P2
Query on ACT

Download Ideal Coordinates CCD File 
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.489α = 90
b = 81.489β = 90
c = 282.224γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1506206
National Science Foundation (NSF, United States)United StatesMCB-1021384

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description