6C3U | pdb_00006c3u

Crystal structure of Klebsiella pneumoniae fosfomycin resistance protein (FosAKP) with inhibitor (ANY2) bound

• PDB DOI: https://doi.org/10.2210/pdb6C3U/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-10 Released: 2018-12-26 
• Deposition Author(s): Klontz, E.H., Sundberg, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Small-Molecule Inhibitor of FosA Expands Fosfomycin Activity to Multidrug-Resistant Gram-Negative Pathogens.

Tomich, A.D., Klontz, E.H., Deredge, D., Barnard, J.P., McElheny, C.L., Eshbach, M.L., Weisz, O.A., Wintrode, P., Doi, Y., Sundberg, E.J., Sluis-Cremer, N.

(2019) Antimicrob Agents Chemother 63

• PubMed: 30642934 
• DOI: https://doi.org/10.1128/AAC.01524-18
• Primary Citation Related Structures: 
  5WEP, 5WEW, 6C3U


• PubMed Abstract: 
  

  The spread of multidrug or extensively drug-resistant Gram-negative bacteria is a serious public health issue. There are too few new antibiotics in development to combat the threat of multidrug-resistant infections, and consequently the rate of increasing antibiotic resistance is outpacing the drug development process. This fundamentally threatens our ability to treat common infectious diseases. Fosfomycin (FOM) has an established track record of safety in humans and is highly active against Escherichia coli , including multidrug-resistant strains. However, many other Gram-negative pathogens, including the "priority pathogens" Klebsiella pneumoniae and Pseudomonas aeruginosa , are inherently resistant to FOM due to the chromosomal fosA gene, which directs expression of a metal-dependent glutathione S -transferase (FosA) that metabolizes FOM. In this study, we describe the discovery and biochemical and structural characterization of ANY1 (3-bromo-6-[3-(3-bromo-2-oxo-1H-pyrazolo[1,5-a]pyrimidin-6-yl)-4-nitro-1H-pyrazol-5-yl]-1H-pyrazolo[1,5-a]pyrimidin-2-one), a small-molecule active-site inhibitor of FosA. Importantly, ANY1 potentiates FOM activity in representative Gram-negative pathogens. Collectively, our study outlines a new strategy to expand FOM activity to a broader spectrum of Gram-negative pathogens, including multidrug-resistant strains.

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Organizational Affiliation: 
• Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA.
Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.
Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA.
Division of Renal-Electrolyte, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA [e-mail] [e-mail].
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA.
Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.85 kDa 
• Atom Count: 5,073 
• Modeled Residue Count: 551 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FosA family fosfomycin resistance glutathione transferase	A, B, C, D	145	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: AGG09_10885, B8011_01255, BL102_0004085, CEO55_05040
UniProt
Find proteins for A0A0H3GM04 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GM04  Go to UniProtKB:  A0A0H3GM04

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NY2 (Subject of Investigation/LOI)	F [auth A], G [auth A], L [auth D], M [auth D]	3-bromo-6-(4-nitro-1H-pyrazol-3-yl)pyrazolo[1,5-a]pyrimidin-2(1H)-one C9 H5 Br N6 O3 GPUSMPJXAIFKFV-UHFFFAOYSA-N
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	E [auth A], H [auth B], J [auth C], K [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.765	α = 90
b = 68.837	β = 90.46
c = 90.312	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Klontz, E.H., Sundberg, E.J.

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Database references
• Version 1.2: 2019-03-13
  Changes: Data collection, Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description