Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.44 kDa 
• Atom Count: 6238 
• Modelled Residue Count: 787 
• Deposited Residue Count: 867 
• Unique protein chains: 1

5FBS

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

• PDB DOI: 10.2210/pdb5FBS/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes serotype 4b str. F2365
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-14 Released: 2016-01-13 
• Deposition Author(s): Stogios, P.J., Wawrzak, Z., Skarina, T., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.318 
• R-Value Work: 0.260 
• R-Value Observed: 0.263 

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

• PubMed: 27103605 
• DOI: 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.

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Organizational Affiliation: 

M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, Ontario, Canada L8S 4K1.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate synthase	A	867	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.318 
• R-Value Work: 0.260 
• R-Value Observed: 0.263 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data DOI: 10.18430/M35FBS Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.51	α = 90
b = 58.51	β = 90
c = 601.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-12-14 
• Released Date: 2016-01-13 
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Skarina, T., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Structure summary
• Version 1.2: 2016-05-04
  Changes: Database references