Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.82 kDa 
• Atom Count: 1823 
• Modelled Residue Count: 192 
• Deposited Residue Count: 209 
• Unique protein chains: 1

3UF8

Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with a G95A surface mutation from Burkholderia pseudomallei complexed with FK506

• PDB DOI: 10.2210/pdb3UF8/pdb

• Classification: Isomerase, protein binding
• Organism(s): Saccharomyces cerevisiae S288C, Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-10-31 Released: 2011-11-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.183 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 

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

• PubMed: 24366729 
• DOI: 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase	A	209	Saccharomyces cerevisiae S288C, Burkholderia pseudomallei 1710b This entity is chimeric	Mutation(s): 1  Gene Names: BURPS1710b_A0907, SMT3, YDR510W, D9719.15 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
UniProt Groups	Q3JK38Q12306

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FK5	B [auth A]	8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN C44 H69 N O12 QJJXYPPXXYFBGM-LFZNUXCKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.183 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 
• Space Group: P 1 2₁ 1
• Diffraction Data DOI: 10.18430/M33UF8 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.4	α = 90
b = 32.77	β = 90.59
c = 76.99	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-31 
• Released Date: 2011-11-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2011-11-30
  Changes: Other, Structure summary
• Version 1.2: 2014-03-12
  Changes: Database references
• Version 1.3: 2014-03-19
  Changes: Other
• Version 1.4: 2017-08-23
  Changes: Refinement description, Source and taxonomy