1GUF | pdb_00001guf

Enoyl thioester reductase from Candida tropicalis

PDB DOI: https://doi.org/10.2210/pdb1GUF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candida tropicalis
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2002-01-25 Released: 2003-03-13
Deposition Author(s): Airenne, T.T., Torkko, J.M., Van Der Plas, S., Sormunen, R.T., Kastaniotis, A.J., Wierenga, R.K., Hiltunen, J.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.215 (Depositor), 0.215 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure-Function Analysis of Enoyl Thioester Reductase Involved in Mitochondrial Maintenance

Airenne, T.T., Torkko, J.M., Van Der Plas, S., Sormunen, R.T., Kastaniotis, A.J., Wierenga, R.K., Hiltunen, J.K.

(2003) J Mol Biology 327: 47

PubMed: 12614607 Search on PubMed
DOI: https://doi.org/10.1016/s0022-2836(03)00038-x
Primary Citation Related Structures:
1GU7, 1GUF, 1GYR

PubMed Abstract:
Candida tropicalis enoyl thioester reductase Etr1p and the Saccharomyces cerevisiae homologue Mrf1p catalyse the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis (FAS). Unlike prokaryotic enoyl thioester reductases (ETRs), which belong to the short-chain dehydrogenases/reductases (SDR), Etr1p and Mrf1p represent structurally distinguishable ETRs that belong to the medium-chain dehydrogenases/reductases (MDR) superfamily, indicating independent origin of two separate classes of ETRs. The crystal structures of Etr1p, the Etr1p-NADPH complex and the Etr1Y79Np mutant were refined to 1.70A, 2.25A and 2.60A resolution, respectively. The native fold of Etr1p was maintained in Etr1Y79Np, but the mutant had only 0.1% of Etr1p catalytic activity remaining and failed to rescue the respiratory deficient phenotype of the mrf1Delta strain. Mutagenesis of Tyr73 in Mrf1p, corresponding to Tyr79 in Etr1p, produced similar results. Our data indicate that the mitochondrial reductase activity is indispensable for respiratory function in yeast, emphasizing the significance of Mrf1p (Etr1p) and mitochondrial FAS for the integrity of the respiratory competent organelle.

Organizational Affiliation

Biocenter Oulu and Department of Biochemistry, P.O. Box 3000, FIN-90014 University of Oulu, Finland.

Macromolecule Content

Total Structure Weight: 81.83 kDa
Atom Count: 6,335
Modeled Residue Count: 728
Deposited Residue Count: 728
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH, B-SPECIFIC] 1, MITOCHONDRIAL	A, B	364	Candida tropicalis	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WZM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B]	I [auth A], Q [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain Q [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A]	F [auth A] G [auth A] H [auth A] J [auth A] K [auth A] F [auth A], G [auth A], H [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	C [auth A], D [auth A], E [auth A], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.215 (Depositor), 0.215 (DCC)
R-Value Work: 0.178 (Depositor), 0.178 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.17	α = 90
b = 92.17	β = 90
c = 225.66	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-03-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-03-13
Type: Initial release
Version 1.1: 2011-08-31
Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
Version 1.2: 2017-06-28
Changes: Data collection
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description