6XRP

Crystal structure of GlpG in complex with peptide ketoamide inhibitor, Ac-RVWHA-ketoamide-phenylbutyl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Designed Parasite-Selective Rhomboid Inhibitors Block Invasion and Clear Blood-Stage Malaria.

Gandhi, S.Baker, R.P.Cho, S.Stanchev, S.Strisovsky, K.Urban, S.

(2020) Cell Chem Biol 27: 1410-1424.e6

  • DOI: https://doi.org/10.1016/j.chembiol.2020.08.011
  • Primary Citation of Related Structures:  
    6VJ8, 6VJ9, 6XRO, 6XRP

  • PubMed Abstract: 

    Rhomboid intramembrane proteases regulate pathophysiological processes, but their targeting in a disease context has never been achieved. We decoded the atypical substrate specificity of malaria rhomboid PfROM4, but found, unexpectedly, that it results from "steric exclusion": PfROM4 and canonical rhomboid proteases cannot cleave each other's substrates due to reciprocal juxtamembrane steric clashes. Instead, we engineered an optimal sequence that enhanced proteolysis >10-fold, and solved high-resolution structures to discover that boronates enhance inhibition >100-fold. A peptide boronate modeled on our "super-substrate" carrying one "steric-excluding" residue inhibited PfROM4 but not human rhomboid proteolysis. We further screened a library to discover an orthogonal alpha-ketoamide that potently inhibited PfROM4 but not human rhomboid proteolysis. Despite the membrane-immersed target and rapid invasion, ultrastructural analysis revealed that single-dosing blood-stage malaria cultures blocked host-cell invasion and cleared parasitemia. These observations establish a strategy for designing parasite-selective rhomboid inhibitors and expose a druggable dependence on rhomboid proteolysis in non-motile parasites.


  • Organizational Affiliation

    Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhomboid protease GlpG211Escherichia coliMutation(s): 0 
Gene Names: glpGSK83_00858
EC: 3.4.21.105
Membrane Entity: Yes 
UniProt
Find proteins for P09391 (Escherichia coli (strain K12))
Explore P09391 
Go to UniProtKB:  P09391
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09391
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide ketoamide inhibitor6Drosophila melanogasterMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V87
Query on V87

Download Ideal Coordinates CCD File 
C [auth B]N-(4-phenylbutyl)formamide
C11 H15 N O
FSDTVSVBONVQBJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.46α = 90
b = 109.46β = 90
c = 129.471γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01AI066025

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description