3UQA

Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation A54E from Burkholderia pseudomallei complexed with FK506


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 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, 3UQB, 3VAW, 4DZ2, 4DZ3, 4FN2, 4G50, 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
209Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Burkholderia pseudomallei (strain K96243)
This entity is chimeric
Gene Names: SMT3, fbp
EC: 5.2.1.8
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12306
Find proteins for Q63J95 (Burkholderia pseudomallei (strain K96243))
Go to UniProtKB:  Q63J95
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5

Download SDF File 
Download CCD File 
A
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
K506
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 96.310α = 90.00
b = 31.280β = 121.57
c = 74.320γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
REFMACphasing
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references
  • Version 1.2: 2014-03-19
    Type: Other
  • Version 1.3: 2017-08-23
    Type: Refinement description, Source and taxonomy