5FBT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.702 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1038/ncomms11343
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoenolpyruvate synthase
A
867Listeria monocytogenes serotype 4b (strain F2365)Mutation(s): 0 
Find proteins for A0A0X1KHF9 (Listeria monocytogenes serotype 4b (strain F2365))
Go to UniProtKB:  A0A0X1KHF9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
5WQ
Query on 5WQ

Download SDF File 
Download CCD File 
A
Rifampin
C43 H64 N4 O11
GKIQTWBZJKGLKG-FVKVYWJVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 149.276α = 90.00
b = 149.276β = 90.00
c = 193.525γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
PHENIXmodel building
HKL-3000data reduction
Cootmodel building
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Structure summary
  • Version 1.2: 2016-05-04
    Type: Database references