6ZE7

Chaetomium thermophilum FAD-dependent oxidoreductase in complex with 4-nitrophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum.

Svecova, L.Ostergaard, L.H.Skalova, T.Schnorr, K.M.Koval', T.Kolenko, P.Stransky, J.Sedlak, D.Duskova, J.Trundova, M.Hasek, J.Dohnalek, J.

(2021) Acta Crystallogr D Struct Biol 77: 755-775

  • DOI: https://doi.org/10.1107/S2059798321003533
  • Primary Citation of Related Structures:  
    6ZE2, 6ZE3, 6ZE4, 6ZE5, 6ZE6, 6ZE7, 7AA2

  • PubMed Abstract: 

    The FAD-dependent oxidoreductase from Chaetomium thermophilum (CtFDO) is a novel thermostable glycoprotein from the glucose-methanol-choline (GMC) oxidoreductase superfamily. However, CtFDO shows no activity toward the typical substrates of the family and high-throughput screening with around 1000 compounds did not yield any strongly reacting substrate. Therefore, protein crystallography, including crystallographic fragment screening, with 42 fragments and 37 other compounds was used to describe the ligand-binding sites of CtFDO and to characterize the nature of its substrate. The structure of CtFDO reveals an unusually wide-open solvent-accessible active-site pocket with a unique His-Ser amino-acid pair putatively involved in enzyme catalysis. A series of six crystal structures of CtFDO complexes revealed five different subsites for the binding of aryl moieties inside the active-site pocket and conformational flexibility of the interacting amino acids when adapting to a particular ligand. The protein is capable of binding complex polyaromatic substrates of molecular weight greater than 500 Da.


  • Organizational Affiliation

    Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Průmyslová 595, 252 50 Vestec, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAD-dependent oxidoreductase
A, B
595Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0048040
UniProt
Find proteins for G0SAW6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SAW6 
Go to UniProtKB:  G0SAW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SAW6
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FDA (Subject of Investigation/LOI)
Query on FDA

Download Ideal Coordinates CCD File 
E [auth A],
U [auth B]
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
V [auth B]
W [auth B]
F [auth A],
G [auth A],
H [auth A],
V [auth B],
W [auth B],
X [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
FA [auth B],
O [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
GA [auth B],
P [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
NPO (Subject of Investigation/LOI)
Query on NPO

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
Y [auth B]
P-NITROPHENOL
C6 H5 N O3
BTJIUGUIPKRLHP-UHFFFAOYSA-N
ACT
Query on ACT

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EA [auth B],
N [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT
Query on FMT

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AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
K [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
K [auth A],
L [auth A],
M [auth A],
Z [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
HA [auth B],
IA [auth B],
Q [auth A],
R [auth A],
S [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
T [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.611α = 90
b = 109.674β = 90
c = 115.634γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development FundCzech RepublicCZ.02.1.01/0.0/0.0/15_003/0000447
European Regional Development FundCzech RepublicCZ.02.1.01/0.0/0.0/16_013/0001776
European Regional Development FundCzech RepublicCZ.1.05/1.1.00/02.0109
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2015043
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2018127
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLQ1604

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description