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

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1128/AAC.01875-13
  • Primary Citation of Related Structures:  
    3UF8, 3UQA, 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase209Saccharomyces cerevisiae S288CBurkholderia pseudomallei 1710b
This entity is chimeric
Mutation(s): 1 
Gene Names: BURPS1710b_A0907SMT3YDR510WD9719.15
Find proteins for Q63J95 (Burkholderia pseudomallei (strain K96243))
Explore Q63J95 
Go to UniProtKB:  Q63J95
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ12306Q63J95
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.31α = 90
b = 31.28β = 121.57
c = 74.32γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
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: 2011-12-07
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2014-03-19
    Changes: Other
  • Version 1.3: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description