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 

wwPDB Validation 3D Report Full Report


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:  3UF8, 3UQA, 3UQB, 3VAW, 4DZ2, 4DZ3, 4FN2, 4GGQ, 4GIV

  • 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 causa ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
A, B
209Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Burkholderia pseudomallei (strain 1710b)
This entity is chimeric
Gene Names: SMT3,
EC: 5.2.1.8
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12306
Find proteins for Q3JK38 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JK38
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
861
Query on 861

Download SDF File 
Download CCD File 
A, B
3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate
C25 H33 N O7 S
WUVVOAPMLQTLBJ-NRFANRHFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 33.630α = 91.54
b = 35.110β = 99.90
c = 75.150γ = 97.23
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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