7S04

1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC) from Acinetobacter baumannii in complex with FR900098, NADPH, and a magnesium ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Characterization and Inhibition of 1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase: A Promising Drug Target in Acinetobacter baumannii and Klebsiella pneumoniae .

Ball, H.S.Girma, M.B.Zainab, M.Soojhawon, I.Couch, R.D.Noble, S.M.

(2021) ACS Infect Dis 7: 2987-2998

  • DOI: https://doi.org/10.1021/acsinfecdis.1c00132
  • Primary Citation of Related Structures:  
    7S04

  • PubMed Abstract: 

    The ESKAPE pathogens comprise a group of multidrug-resistant bacteria that are the leading cause of nosocomial infections worldwide. The prevalence of antibiotic resistant strains and the relative ease by which bacteria acquire resistance genes highlight the continual need for the development of novel antibiotics against new drug targets. The methylerythritol phosphate (MEP) pathway is an attractive target for the development of new antibiotics. The MEP pathway governs the synthesis of isoprenoids, which are key lipid precursors for vital cell components such as ubiquinone and bacterial hopanoids. Additionally, the MEP pathway is entirely distinct from the corresponding mammalian pathway, the mevalonic acid (MVA) pathway, making the first committed enzyme of the MEP pathway, 1-deoxy-d-xylulose 5-phosphate reductoisomerase (IspC), an attractive target for antibiotic development. To facilitate drug development against two of the ESKAPE pathogens, Acinetobacter baumannii and Klebsiella pneumoniae , we cloned, expressed, purified, and characterized IspC from these two Gram-negative bacteria. Enzyme inhibition assays using IspC from these two pathogens, and compounds fosmidomycin and FR900098, indicate IC 50 values ranging from 19.5-45.5 nM. Antimicrobial susceptibility tests with these inhibitors reveal that A. baumannii is susceptible to FR900098, whereas K. pneumoniae is susceptible to both compounds. Finally, to facilitate structure-based drug design of inhibitors targeting A. baumannii IspC, we determined the 2.5 Å crystal structure of IspC from A. baumannii in complex with inhibitor FR900098, and cofactors NADPH and magnesium.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20109, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-deoxy-D-xylulose 5-phosphate reductoisomerase406Acinetobacter baumanniiMutation(s): 0 
Gene Names: 
EC: 1.1.1.267
UniProt
Find proteins for B7H1U5 (Acinetobacter baumannii (strain AB307-0294))
Explore B7H1U5 
Go to UniProtKB:  B7H1U5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7H1U5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
D [auth A]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
F98 (Subject of Investigation/LOI)
Query on F98

Download Ideal Coordinates CCD File 
B [auth A]3-[ethanoyl(hydroxy)amino]propylphosphonic acid
C5 H12 N O5 P
PKMNDDZSIHLLLI-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.572α = 90
b = 118.251β = 90
c = 53.911γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentW81XWH-17-C-0066
Other governmentW0083_13_WR

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description