4G50

Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation D44G from Burkholderia pseudomallei complexed with CJ168


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins.

Begley, D.W.Fox, D.Jenner, D.Juli, C.Pierce, P.G.Abendroth, J.Muruthi, M.Safford, K.Anderson, V.Atkins, K.Barnes, S.R.Moen, S.O.Raymond, A.C.Stacy, R.Myler, P.J.Staker, B.L.Harmer, N.J.Norville, I.H.Holzgrabe, U.Sarkar-Tyson, M.Edwards, T.E.Lorimer, D.D.

(2014) Antimicrob Agents Chemother 58: 1458-1467

  • DOI: 10.1128/AAC.01875-13
  • Primary Citation of Related Structures:  
    4G50, 4GGQ, 4GIV, 3UQA, 3UQB, 3UF8, 3VAW, 4DZ2, 4DZ3, 4FN2

  • PubMed Abstract: 
  • Macrophage infectivity potentiators (Mips) are immunophilin proteins and essential virulence factors for a range of pathogenic organisms. We applied a structural biology approach to characterize a Mip from Burkholderia pseudomallei (BpML1), the causative agent of melioidosis ...

    Macrophage infectivity potentiators (Mips) are immunophilin proteins and essential virulence factors for a range of pathogenic organisms. We applied a structural biology approach to characterize a Mip from Burkholderia pseudomallei (BpML1), the causative agent of melioidosis. Crystal structure and nuclear magnetic resonance analyses of BpML1 in complex with known macrocyclics and other derivatives led to the identification of a key chemical scaffold. This scaffold possesses inhibitory potency for BpML1 without the immunosuppressive components of related macrocyclic agents. Biophysical characterization of a compound series with this scaffold allowed binding site specificity in solution and potency determinations for rank ordering the set. The best compounds in this series possessed a low-micromolar affinity for BpML1, bound at the site of enzymatic activity, and inhibited a panel of homologous Mip proteins from other pathogenic bacteria, without demonstrating toxicity in human macrophages. Importantly, the in vitro activity of BpML1 was reduced by these compounds, leading to decreased macrophage infectivity and intracellular growth of Burkholderia pseudomallei. These compounds offer the potential for activity against a new class of antimicrobial targets and present the utility of a structure-based approach for novel antimicrobial drug discovery.


    Organizational Affiliation

    Emerald Bio, Bainbridge Island, Washington, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomeraseA, B209Saccharomyces cerevisiae S288CBurkholderia pseudomallei 1710b
This entity is chimeric
Mutation(s): 1 
Gene Names: BURPS1710b_A0907SMT3YDR510WD9719.15
EC: 5.2.1.8
UniProt
Find proteins for Q3JK38 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JK38 
Go to UniProtKB:  Q3JK38
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
861 (Subject of Investigation/LOI)
Query on 861

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate
C25 H33 N O7 S
WUVVOAPMLQTLBJ-NRFANRHFSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth B], J [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], H [auth B], I [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/M34G50 Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.63α = 91.54
b = 35.11β = 99.9
c = 75.15γ = 97.23
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Refinement description, Source and taxonomy