8OK0

Crystal structure of human NQO1 in complex with the inhibitor PMSF

PDB DOI: https://doi.org/10.2210/pdb8OK0/pdb

Classification: FLAVOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-26 Released: 2023-11-01
Deposition Author(s): Martin-Garcia, J.M., Grieco, A., Ruiz-Fresneda, M.A.
Funding Organization(s): Comunidad de Madrid

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.247
R-Value Work: 0.208
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural dynamics at the active site of the cancer-associated flavoenzyme NQO1 probed by chemical modification with PMSF.

Grieco, A., Ruiz-Fresneda, M.A., Gomez-Mulas, A., Pacheco-Garcia, J.L., Quereda-Moraleda, I., Pey, A.L., Martin-Garcia, J.M.

(2023) FEBS Lett 597: 2687-2698

PubMed: 37726177 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.14738
Primary Citation of Related Structures:
8OK0

PubMed Abstract:
A large conformational heterogeneity of human NAD(P)H:quinone oxidoreductase 1 (NQO1), a flavoprotein associated with various human diseases, has been observed to occur in the catalytic site of the enzyme. Here, we report the X-ray structure of NQO1 with phenylmethylsulfonyl fluoride (PMSF) at 1.6 Å resolution. Activity assays confirmed that, despite being covalently bound to the Tyr128 residue at the catalytic site, PMSF did not abolish NQO1 activity. This may indicate that the PMSF molecule does not reduce the high flexibility of Tyr128, thus allowing NADH and DCPIP substrates to bind to the enzyme. Our results show that targeting Tyr128, a key residue in NQO1 function, with small covalently bound molecules could possibly not be a good drug discovery strategy to inhibit this enzyme.

Organizational Affiliation

Department of Crystallography & Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain.

Macromolecule Content

Total Structure Weight: 127.8 kDa
Atom Count: 10,093
Modelled Residue Count: 1,084
Deposited Residue Count: 1,092
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H dehydrogenase [quinone] 1	A, B [auth D], C [auth B], D [auth C]	273	Homo sapiens	Mutation(s): 0 Gene Names: NQO1
UniProt & NIH Common Fund Data Resources
Find proteins for P15559 (Homo sapiens) Explore P15559 Go to UniProtKB: P15559
PHAROS: P15559 GTEx: ENSG00000181019
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15559
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth D] SDF format, chain M [auth B] SDF format, chain R [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth D] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C]	E [auth A], I [auth D], M [auth B], R [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth D] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth D] Focus chain M [auth B] Focus chain R [auth C]
PMS Query on PMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth D] SDF format, chain N [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth D] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C]	F [auth A], J [auth D], N [auth B], Q [auth B], S [auth C]	phenylmethanesulfonic acid C₇ H₈ O₃ S NIXKBAZVOQAHGC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth D] Focus chain N [auth B] Focus chain Q [auth B] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth D] Focus chain N [auth B] Focus chain Q [auth B] Focus chain S [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth D] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth D] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C]	G [auth A] K [auth D] O [auth B] T [auth C] U [auth C] G [auth A], K [auth D], O [auth B], T [auth C], U [auth C], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth D] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth D] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
ACE Query on ACE Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth D] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth D] MOL2 format, chain P [auth B]	H [auth A], L [auth D], P [auth B]	ACETYL GROUP C₂ H₄ O IKHGUXGNUITLKF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth D] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth D] Focus chain P [auth B]