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- PDB-5a4k: Crystal structure of the R139W variant of human NAD(P)H:quinone o... -

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Basic information

Entry
Database: PDB / ID: 5a4k
TitleCrystal structure of the R139W variant of human NAD(P)H:quinone oxidoreductase
ComponentsNAD(P)H DEHYDROGENASE [QUINONE] 1
KeywordsOXIDOREDUCTASE / NQO1 / FAD / FLAVOPROTEIN / OXIDATIVE STRESS / QUINONE REDUCTASE / DRUG METABOLISM / SINGLE AMINO ACID EXCHANGE
Function / homology
Function and homology information


ubiquinone metabolic process / vitamin E metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / cytochrome-b5 reductase activity, acting on NAD(P)H / vitamin K metabolic process / NADH dehydrogenase (quinone) (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) ...ubiquinone metabolic process / vitamin E metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / cytochrome-b5 reductase activity, acting on NAD(P)H / vitamin K metabolic process / NADH dehydrogenase (quinone) (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of ferroptosis / nitric oxide biosynthetic process / xenobiotic metabolic process / removal of superoxide radicals / cell redox homeostasis / protein catabolic process / negative regulation of protein catabolic process / response to toxic substance / protein polyubiquitination / response to oxidative stress / cellular response to oxidative stress / response to lipopolysaccharide / innate immune response / synapse / RNA binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.093 Å
AuthorsLienhart, W.D. / Strandback, E. / Gudipati, V. / Uhl, M.K. / Rantase, D.M. / Zangger, K. / Gruber, K. / Macheroux, P.
CitationJournal: FEBS J. / Year: 2017
Title: Catalytic competence, structure and stability of the cancer-associated R139W variant of the human NAD(P)H:quinone oxidoreductase 1 (NQO1).
Authors: Lienhart, W.D. / Strandback, E. / Gudipati, V. / Koch, K. / Binter, A. / Uhl, M.K. / Rantasa, D.M. / Bourgeois, B. / Madl, T. / Zangger, K. / Gruber, K. / Macheroux, P.
History
DepositionJun 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)H DEHYDROGENASE [QUINONE] 1
B: NAD(P)H DEHYDROGENASE [QUINONE] 1
C: NAD(P)H DEHYDROGENASE [QUINONE] 1
D: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,99310
Polymers132,4324
Non-polymers3,5616
Water18,9521052
1
B: NAD(P)H DEHYDROGENASE [QUINONE] 1
C: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9965
Polymers66,2162
Non-polymers1,7803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-50 kcal/mol
Surface area21510 Å2
MethodPISA
2
A: NAD(P)H DEHYDROGENASE [QUINONE] 1
D: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9965
Polymers66,2162
Non-polymers1,7803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-49.8 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.606, 56.928, 99.827
Angle α, β, γ (deg.)100.37, 92.85, 90.22
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.993274, 0.05409, 0.102374), (0.050005, -0.597062, 0.800635), (0.10443, 0.800369, 0.590342)16.719, 17.47, -9.931
2given(-0.992907, -0.056015, -0.104869), (-0.050851, -0.597219, 0.800464), (-0.107468, 0.800119, 0.590135)31.852, 35.016, -15.518

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Components

#1: Protein
NAD(P)H DEHYDROGENASE [QUINONE] 1 / AZOREDUCTASE / DT-DIAPHORASE / DTD / MENADIONE REDUCTASE / NAD(P)H\:QUINONE OXIDOREDUCTASE 1 / ...AZOREDUCTASE / DT-DIAPHORASE / DTD / MENADIONE REDUCTASE / NAD(P)H\:QUINONE OXIDOREDUCTASE 1 / PHYLLOQUINONE REDUCTASE / QUINONE REDUCTASE 1 / QR1 / NADPH QUINONE OXIDOREDUCTASE


Mass: 33107.984 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P15559, NAD(P)H dehydrogenase (quinone)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1052 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HIS-TAG AND CLEAVAGE SITE R139W VARIANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.57 % / Description: NONE
Crystal growDetails: 200 MM LI2SO4, 100 MM BISTRIS (PH 6.5), 25% W/V PEG 3350, PROTEIN CONCENTRATION: 6.1 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Details: TOROIDAL FOCUSING
RadiationMonochromator: BARTELS MONOCHROMATOR, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→49.03 Å / Num. obs: 67587 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.27
Reflection shellResolution: 2.09→2.17 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBG

1qbg


Resolution: 2.093→49.033 Å / SU ML: 0.22 / σ(F): 1.97 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 3418 5.1 %
Rwork0.1693 --
obs0.1709 67536 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.093→49.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8644 0 240 1052 9936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039160
X-RAY DIFFRACTIONf_angle_d0.95112429
X-RAY DIFFRACTIONf_dihedral_angle_d15.8983333
X-RAY DIFFRACTIONf_chiral_restr0.1041299
X-RAY DIFFRACTIONf_plane_restr0.0031545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0932-2.12310.3198950.26212016X-RAY DIFFRACTION73
2.1231-2.15480.2391510.2152646X-RAY DIFFRACTION97
2.1548-2.18850.25321660.20862724X-RAY DIFFRACTION97
2.1885-2.22430.2981410.2072584X-RAY DIFFRACTION97
2.2243-2.26270.25831360.22735X-RAY DIFFRACTION97
2.2627-2.30380.21941390.19712648X-RAY DIFFRACTION97
2.3038-2.34810.2351660.18652664X-RAY DIFFRACTION97
2.3481-2.39610.22551340.18392697X-RAY DIFFRACTION97
2.3961-2.44820.21761170.17772697X-RAY DIFFRACTION98
2.4482-2.50510.23431410.18522694X-RAY DIFFRACTION98
2.5051-2.56780.20991380.17192752X-RAY DIFFRACTION98
2.5678-2.63720.19721440.18082700X-RAY DIFFRACTION98
2.6372-2.71480.19921310.18152726X-RAY DIFFRACTION98
2.7148-2.80240.23371500.17782679X-RAY DIFFRACTION98
2.8024-2.90250.24251500.18852689X-RAY DIFFRACTION98
2.9025-3.01870.21151760.17882709X-RAY DIFFRACTION98
3.0187-3.15610.19081350.17332706X-RAY DIFFRACTION98
3.1561-3.32250.18561530.1722706X-RAY DIFFRACTION99
3.3225-3.53060.18581250.15122722X-RAY DIFFRACTION99
3.5306-3.80310.17711340.14442737X-RAY DIFFRACTION99
3.8031-4.18560.17591330.13912727X-RAY DIFFRACTION99
4.1856-4.79080.14431500.12972703X-RAY DIFFRACTION99
4.7908-6.03420.17021640.14882741X-RAY DIFFRACTION99
6.0342-49.04640.18041490.16942716X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1215-0.09140.08310.83340.2731.4014-0.0378-0.1369-0.07110.0848-0.02280.10280.122-0.25420.03780.1415-0.01930.02080.191400.15050.661820.478833.1882
21.8523-0.24540.39691.05890.76791.4266-0.1863-0.40460.3470.1855-0.01040.0978-0.2632-0.39780.19660.28280.0527-0.01650.3764-0.08570.22540.508240.509648.274
30.93780.1715-0.07170.5870.14091.4466-0.01910.1720.1269-0.0745-0.01750.0742-0.11-0.26530.02620.15190.0323-0.0140.1960.00510.16585.868823.6081-10.494
41.56160.1478-0.33610.60420.57151.2073-0.08950.4333-0.3099-0.1649-0.09930.10590.2918-0.27240.17080.276-0.06360.010.3743-0.10280.21115.7833.581-25.4278
50.9853-0.0902-0.03831.35080.14510.93460.0002-0.03080.02550.07570.0097-0.1456-0.07170.0736-0.00940.1501-0.0085-0.00030.1106-0.00180.155226.861118.17581.1224
61.14750.01720.07370.88380.05111.263-0.06080.2227-0.1178-0.13080.0091-0.12350.06210.08920.04420.1732-0.00910.03370.1736-0.04670.179225.80416.9633-15.8221
70.89360.02560.10141.39610.22650.8166-0.00550.0312-0.0512-0.04310.0276-0.10950.05280.0826-0.00130.13230.01810.00290.09580.01020.127521.635925.880221.627
81.1195-0.0156-0.03960.99680.04391.1242-0.0303-0.1870.1090.13840.0186-0.0994-0.05280.08320.00510.1760.016-0.02040.1728-0.03890.163220.535137.021638.6394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:223)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 224:274)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 3:223)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 224:274)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 3:128)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 129:273)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 3:128)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 129:272)

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