3KRZ

Crystal Structure of the Thermostable NADH4-bound old yellow enzyme from Thermoanaerobacter pseudethanolicus E39

PDB DOI: https://doi.org/10.2210/pdb3KRZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermoanaerobacter pseudethanolicus ATCC 33223
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-20 Released: 2009-12-08
Deposition Author(s): Adalbjornsson, B.V., Toogood, H.S., Leys, D., Scrutton, N.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.194
R-Value Work: 0.157
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Biocatalysis with thermostable enzymes: structure and properties of a thermophilic 'ene'-reductase related to old yellow enzyme.

Adalbjornsson, B.V., Toogood, H.S., Fryszkowska, A., Pudney, C.R., Jowitt, T.A., Leys, D., Scrutton, N.S.

(2010) Chembiochem 11: 197-207

PubMed: 19943268 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200900570
Primary Citation of Related Structures:
3KRU, 3KRZ

PubMed Abstract:
We report the crystal structure of a thermophilic "ene" reductase (TOYE) isolated from Thermoanaerobacter pseudethanolicus E39. The crystal structure reveals a tetrameric enzyme and an active site that is relatively large compared to most other structurally determined and related Old Yellow Enzymes. The enzyme adopts higher order oligomeric states (octamers and dodecamers) in solution, as revealed by sedimentation velocity and multiangle laser light scattering. Bead modelling indicates that the solution structure is consistent with the basic tetrameric structure observed in crystallographic studies and electron microscopy. TOYE is stable at high temperatures (T(m)>70 degrees C) and shows increased resistance to denaturation in water-miscible organic solvents compared to the mesophilic Old Yellow Enzyme family member, pentaerythritol tetranitrate reductase. TOYE has typical ene-reductase properties of the Old Yellow Enzyme family. There is currently major interest in using Old Yellow Enzyme family members in the preparative biocatalysis of a number of activated alkenes. The increased stability of TOYE in organic solvents is advantageous for biotransformations in which water-miscible organic solvents and biphasic reaction conditions are required to both deliver novel substrates and minimize product racemisation.

Organizational Affiliation

Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

Macromolecule Content

Total Structure Weight: 157.4 kDa
Atom Count: 12,695
Modelled Residue Count: 1,338
Deposited Residue Count: 1,348
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:flavin oxidoreductase/NADH oxidase	A, B, C, D	337	Thermoanaerobacter pseudethanolicus ATCC 33223	Mutation(s): 0 Gene Names: Teth39_0012, ZP_00777979
UniProt
Find proteins for B0KAH1 (Thermoanaerobacter pseudethanolicus (strain ATCC 33223 / 39E)) Explore B0KAH1 Go to UniProtKB: B0KAH1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B0KAH1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TXD Query on TXD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₃₁ N₇ O₁₄ P₂ GFDCQHGWOHYWLP-BFAIWXBASA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.194
R-Value Work: 0.157
R-Value Observed: 0.157
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.38	α = 90
b = 98.556	β = 92.4
c = 95.134	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-12-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations