5CP8

The effect of isoleucine to alanine mutation on InhA enzyme crystallization pattern and substrate binding loop conformation and flexibility


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA.

Lai, C.T.Li, H.J.Yu, W.Shah, S.Bommineni, G.R.Perrone, V.Garcia-Diaz, M.Tonge, P.J.Simmerling, C.

(2015) Biochemistry 54: 4683-4691

  • DOI: 10.1021/acs.biochem.5b00284
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Slow-onset enzyme inhibitors are the subject of considerable interest as an approach to increasing the potency of pharmaceutical compounds by extending the residence time of the inhibitor on the target (the lifetime of the drug-receptor complex). How ...

    Slow-onset enzyme inhibitors are the subject of considerable interest as an approach to increasing the potency of pharmaceutical compounds by extending the residence time of the inhibitor on the target (the lifetime of the drug-receptor complex). However, rational modulation of residence time presents significant challenges because it requires additional mechanistic insight, such as the nature of the transition state for postbinding isomerization. Our previous work, based on X-ray crystallography, enzyme kinetics, and molecular dynamics simulation, suggested that the slow step in inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA involves a change in the conformation of the substrate binding loop from an open state in the initial enzyme-inhibitor complex to a closed state in the final enzyme-inhibitor complex. Here, we use multidimensional free energy landscapes for loop isomerization to obtain a computational model for the transition state. The results suggest that slow-onset inhibitors crowd key side chains on helices that slide past each other during isomerization, resulting in a steric clash. The landscapes become significantly flatter when residues involved in the steric clash are replaced with alanine. Importantly, this lower barrier can be increased by rational inhibitor redesign to restore the steric clash. Crystallographic studies and enzyme kinetics confirm the predicted effects on loop structure and flexibility, as well as inhibitor residence time. These loss and regain of function studies validate our mechanistic hypothesis for interactions controlling substrate binding loop isomerization, providing a platform for the future design of inhibitors with longer residence times and better in vivo potency. Similar opportunities for slow-onset inhibition via the same mechanism are identified in other pathogens.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enoyl-[acyl-carrier-protein] reductase [NADH]
A
289Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 1 
Gene Names: inhA
EC: 1.3.1.9
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGR1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ETE
Query on ETE

Download SDF File 
Download CCD File 
A
2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
TCU
Query on TCU

Download SDF File 
Download CCD File 
A
5-HEXYL-2-(2-METHYLPHENOXY)PHENOL
2-(O-TOLYLOXY)-5-HEXYLPHENOL
C19 H24 O2
KSWHNTPMGZKIOB-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TCUIC50: 22 nM (99) BINDINGDB
TCUKi: 1571 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 99.794α = 90.00
b = 99.794β = 90.00
c = 139.785γ = 120.00
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2015-09-23
    Type: Other, Structure summary
  • Version 1.3: 2017-11-22
    Type: Derived calculations, Refinement description