5LB9 | pdb_00005lb9

Structure of the T175V Etr1p mutant in the monoclinic form P21

• PDB DOI: https://doi.org/10.2210/pdb5LB9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Candida tropicalis
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2016-06-15 Released: 2017-05-10 
• Deposition Author(s): Wagner, T., Rosenthal, R.G., Voegeli, B., Shima, S., Erb, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.186 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

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

• PubMed: 28504678 
• DOI: https://doi.org/10.1038/nchembio.2375
• Primary Citation 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.

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Organizational Affiliation: 
• Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 86.79 kDa 
• Atom Count: 6,294 
• Modeled Residue Count: 730 
• Deposited Residue Count: 770 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial	A, B	385	Candida tropicalis	Mutation(s): 1  Gene Names: ETR1 EC: 1.3.1.10 (PDB Primary Data), 1.3.1.38 (PDB Primary Data), 1.3.1.104 (UniProt)
UniProt
Find proteins for Q8WZM3 (Candida tropicalis) Explore Q8WZM3  Go to UniProtKB:  Q8WZM3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	G [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
SO4	D [auth A], E [auth A], F [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], S [auth B], T [auth B], U [auth B], V [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], Y [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	N [auth A], W [auth B], X [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.186 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.416	α = 90
b = 101.861	β = 101.01
c = 81.593	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Wagner, T., Rosenthal, R.G., Voegeli, B., Shima, S., Erb, T.J.

Revision History  

• 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