4WAS | pdb_00004was

STRUCTURE OF THE ETR1P/NADP/CROTONYL-COA COMPLEX

PDB DOI: https://doi.org/10.2210/pdb4WAS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candida tropicalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-31 Released: 2015-03-18
Deposition Author(s): Quade, N., Voegeli, B., Rosenthal, R., Capitani, G., Erb, T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.224 (Depositor), 0.237 (DCC)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

The use of ene adducts to study and engineer enoyl-thioester reductases.

Rosenthal, R.G., Vogeli, B., Quade, N., Capitani, G., Kiefer, P., Vorholt, J.A., Ebert, M.O., Erb, T.J.

(2015) Nat Chem Biol 11: 398-400

PubMed: 25867044 Search on PubMed
DOI: https://doi.org/10.1038/nchembio.1794
Primary Citation Related Structures:
4W99, 4WAS

PubMed Abstract:
An improved understanding of enzymes' catalytic proficiency and stereoselectivity would further enable applications in chemistry, biocatalysis and industrial biotechnology. We use a chemical probe to dissect individual catalytic steps of enoyl-thioester reductases (Etrs), validating an active site tyrosine as the cryptic proton donor and explaining how it had eluded definitive identification. This information enabled the rational redesign of Etr, yielding mutants that create products with inverted stereochemistry at wild type-like turnover frequency.

Organizational Affiliation

Institute of Microbiology, ETH (Swiss Federal Institute of Technology) Zurich, Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 123.4 kDa
Atom Count: 9,097
Modeled Residue Count: 1,092
Deposited Residue Count: 1,092
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, C	364	Candida tropicalis	Mutation(s): 0 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
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COO Query on COO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C]	E [auth A], G [auth B], I [auth C]	CROTONYL COENZYME A C₂₅ H₄₀ N₇ O₁₇ P₃ S KFWWCMJSYSSPSK-XBTRWLRFSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C]
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C]	D [auth A], F [auth B], H [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.224 (Depositor), 0.237 (DCC)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.188 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.92	α = 90
b = 106.14	β = 98.41
c = 94.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-03-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-03-18
Type: Initial release
Version 1.1: 2015-04-15
Changes: Database references
Version 1.2: 2015-04-22
Changes: Database references
Version 1.3: 2015-05-27
Changes: Database references
Version 2.0: 2024-01-10
Changes: Atomic model, Data collection, Database references, Refinement description