1N9G | pdb_00001n9g

Mitochondrial 2-enoyl thioester reductase Etr1p/Etr2p heterodimer from Candida tropicalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.235 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Candida tropicalis expresses two mitochondrial 2-enoyl thioester reductases that are able to form both homodimers and heterodimers.

Torkko, J.M.Koivuranta, K.T.Kastaniotis, A.J.Airenne, T.T.Glumoff, T.Ilves, M.Hartig, A.Gurvitz, A.Hiltunen, J.K.

(2003) J Biological Chem 278: 41213-41220

  • DOI: https://doi.org/10.1074/jbc.M307664200
  • Primary Citation Related Structures: 
    1N9G

  • PubMed Abstract: 

    Here we report on the cloning of a Candida tropicalis gene, ETR2, that is closely related to ETR1. Both genes encode enzymatically active 2-enoyl thioester reductases involved in mitochondrial synthesis of fatty acids (fatty acid synthesis type II) and respiratory competence. The 5'- and 3'-flanking (coding) regions of ETR2 and ETR1 are about 90% (97%) identical, indicating that the genes have evolved via gene duplication. The gene products differ in three amino acid residues: Ile67 (Val), Ala92 (Thr), and Lys251 (Arg) in Etr2p (Etr1p). Quantitative PCR analysis and reverse transcriptase-PCR indicated that both genes were expressed about equally in fermenting and ETR1 predominantly respiring yeast cells. Like the situation with ETR1, expression of ETR2 in respiration-deficient Saccharomyces cerevisiae mutant cells devoid of Ybr026p/Etr1p was able to restore growth on glycerol. Triclosan that is used as an antibacterial agent against fatty acid synthesis type II 2-enoyl thioester reductases inhibited growth of FabI overexpressing mutant yeast cells but was not able to inhibit respiratory growth of the ETR2- or ETR1-complemented mutant yeast cells. Resolving of crystal structures obtained via Etr2p and Etr1p co-crystallization indicated that all possible dimer variants occur in the same asymmetric unit, suggesting that similar dimer formation also takes place in vivo.


  • Organizational Affiliation
    • Biocenter Oulu, Department of Biochemistry, University of Oulu, Finland.

Macromolecule Content 

  • Total Structure Weight: 255.99 kDa 
  • Atom Count: 18,417 
  • Modeled Residue Count: 2,184 
  • Deposited Residue Count: 2,316 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2,4-dienoyl-CoA reductase
A, C, F
386Candida tropicalisMutation(s): 0 
Gene Names: ETR2
EC: 1.3.1.104
UniProt
Find proteins for Q8WZM4 (Candida tropicalis)
Explore Q8WZM4 
Go to UniProtKB:  Q8WZM4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WZM4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
2,4-dienoyl-CoA reductase
B, D, E
386Candida tropicalisMutation(s): 0 
Gene Names: ETR1
EC: 1.3.1.104
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP

Query on NAP



Download:Ideal Coordinates CCD File
H [auth A],
J [auth B],
O [auth E]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
I [auth B]
K [auth C]
L [auth D]
M [auth D]
G [auth A],
I [auth B],
K [auth C],
L [auth D],
M [auth D],
N [auth E],
P [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.235 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 229.453α = 90
b = 95.501β = 124.71
c = 164.229γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Advisory, Data collection
  • Version 1.4: 2023-08-16
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-12-25
    Changes: Derived calculations, Structure summary