5M0Z | pdb_00005m0z

Cyclohexanone Monooxygenase from T. municipale: reduced enzyme bound to NADP+

PDB DOI: https://doi.org/10.2210/pdb5M0Z/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermocrispum municipale DSM 44069
Expression System: Escherichia coli str. K-12 substr. DH10B
Mutation(s): No

Deposited: 2016-10-06 Released: 2016-12-07
Deposition Author(s): Gomez-Castellanos, J.R., Mattevi, A.
Funding Organization(s): EU Horizon 2020 Programme Research and Innovation actions H2020-LEIT BIO-2014-1

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.177 (Depositor)
R-Value Work:
0.148 (Depositor)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase.

Romero, E., Castellanos, J.R., Mattevi, A., Fraaije, M.W.

(2016) Angew Chem Int Ed Engl 55: 15852-15855

PubMed: 27873437 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.201608951
Primary Citation Related Structures:
5M0Z, 5M10

PubMed Abstract:
Cyclohexanone monooxygenase (CHMO) is a promising biocatalyst for industrial reactions owing to its broad substrate spectrum and excellent regio-, chemo-, and enantioselectivity. However, the low stability of many Baeyer-Villiger monooxygenases is an obstacle for their exploitation in industry. Characterization and crystal structure determination of a robust CHMO from Thermocrispum municipale is reported. The enzyme efficiently converts a variety of aliphatic, aromatic, and cyclic ketones, as well as prochiral sulfides. A compact substrate-binding cavity explains its preference for small rather than bulky substrates. Small-scale conversions with either purified enzyme or whole cells demonstrated the remarkable properties of this newly discovered CHMO. The exceptional solvent tolerance and thermostability make the enzyme very attractive for biotechnology.

Organizational Affiliation

Department of Biotechnology, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands.

Macromolecule Content

Total Structure Weight: 61.79 kDa
Atom Count: 5,096
Modeled Residue Count: 529
Deposited Residue Count: 541
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclohexanone Monooxygenase from Thermocrispum municipale.	A	541	Thermocrispum municipale DSM 44069	Mutation(s): 0 EC: 1.14.13.22
UniProt
Find proteins for A0A1L1QK39 (Thermocrispum municipale DSM 44069) Explore A0A1L1QK39 Go to UniProtKB: A0A1L1QK39
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1L1QK39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA7 Query on NA7 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE C₁₅ H₂₄ N₅ O₁₆ P₃ XDDBFIXGEVGCEU-AOOZFPJJSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.177 (Depositor)
R-Value Work: 0.148 (Depositor)
R-Value Observed: 0.149 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.206	α = 90
b = 114.677	β = 90
c = 155.435	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

Gomez-Castellanos, J.R.

Mattevi, A.

Funding Organization	Location	Grant Number
EU Horizon 2020 Programme Research and Innovation actions H2020-LEIT BIO-2014-1		635734

Revision History (Full details and data files)

Version 1.0: 2016-12-07
Type: Initial release
Version 1.1: 2016-12-21
Changes: Database references
Version 2.0: 2020-04-22
Changes: Atomic model, Database references
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description