Crystal structure of rifampin phosphotransferase RPH-Lm from Listeria monocytogenes in complex with rifampin-phosphate

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Rifampin phosphotransferase is an unusual antibiotic resistance kinase.

Stogios, P.J.Cox, G.Spanogiannopoulos, P.Pillon, M.C.Waglechner, N.Skarina, T.Koteva, K.Guarne, A.Savchenko, A.Wright, G.D.

(2016) Nat Commun 7: 11343-11343

  • DOI: https://doi.org/10.1038/ncomms11343
  • Primary Citation of Related Structures:  
    5FBS, 5FBT, 5FBU

  • PubMed Abstract: 

    Rifampin (RIF) phosphotransferase (RPH) confers antibiotic resistance by conversion of RIF and ATP, to inactive phospho-RIF, AMP and Pi. Here we present the crystal structure of RPH from Listeria monocytogenes (RPH-Lm), which reveals that the enzyme is comprised of three domains: two substrate-binding domains (ATP-grasp and RIF-binding domains); and a smaller phosphate-carrying His swivel domain. Using solution small-angle X-ray scattering and mutagenesis, we reveal a mechanism where the swivel domain transits between the spatially distinct substrate-binding sites during catalysis. RPHs are previously uncharacterized dikinases that are widespread in environmental and pathogenic bacteria. These enzymes are members of a large unexplored group of bacterial enzymes with substrate affinities that have yet to be fully explored. Such an enzymatically complex mechanism of antibiotic resistance augments the spectrum of strategies used by bacteria to evade antimicrobial compounds.

  • Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada M5G 1L6.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoenolpyruvate synthase867Listeria monocytogenes serotype 4b str. F2365Mutation(s): 0 
Gene Names: LmNIHS28_01948
Find proteins for A0A0X1KHF9 (Listeria monocytogenes serotype 4b (strain F2365))
Explore A0A0X1KHF9 
Go to UniProtKB:  A0A0X1KHF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0X1KHF9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.63α = 90
b = 151.63β = 90
c = 191.51γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Structure summary
  • Version 1.2: 2016-05-04
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description