5LBX

Structure of the T175V Etr1p mutant in the trigonal form P312 in complex with NADP and crotonyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A conserved threonine prevents self-intoxication of enoyl-thioester reductases.

Rosenthal, R.G.Vogeli, B.Wagner, T.Shima, S.Erb, T.J.

(2017) Nat Chem Biol 13: 745-749

  • DOI: https://doi.org/10.1038/nchembio.2375
  • Primary Citation of Related Structures:  
    5LB9, 5LBX

  • PubMed Abstract: 

    Enzymes are highly specific biocatalysts, yet they can promote unwanted side reactions. Here we investigated the factors that direct catalysis in the enoyl-thioester reductase Etr1p. We show that a single conserved threonine is essential to suppress the formation of a side product that would otherwise act as a high-affinity inhibitor of the enzyme. Substitution of this threonine with isosteric valine increases side-product formation by more than six orders of magnitude, while decreasing turnover frequency by only one order of magnitude. Our results show that the promotion of wanted reactions and the suppression of unwanted side reactions operate independently at the active site of Etr1p, and that the active suppression of side reactions is highly conserved in the family of medium-chain dehydrogenases/reductases (MDRs). Our discovery emphasizes the fact that the active destabilization of competing transition states is an important factor during catalysis that has implications for the understanding and the de novo design of enzymes.


  • Organizational Affiliation

    Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial
A, B
385Candida tropicalisMutation(s): 1 
Gene Names: ETR1
EC: 1.3.1.10 (PDB Primary Data), 1.3.1.38 (PDB Primary Data)
UniProt
Find proteins for Q8WZM3 (Candida tropicalis)
Explore Q8WZM3 
Go to UniProtKB:  Q8WZM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WZM3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COO
Query on COO

Download Ideal Coordinates CCD File 
L [auth A],
T [auth B]
CROTONYL COENZYME A
C25 H40 N7 O17 P3 S
KFWWCMJSYSSPSK-XBTRWLRFSA-N
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
SO4
Query on SO4

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D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.498α = 90
b = 93.498β = 90
c = 231.203γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references
  • Version 1.2: 2017-06-28
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description