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- PDB-6j7i: Fusion protein of heme oxygenase-1 and NADPH cytochrome P450 redu... -

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Basic information

Entry
Database: PDB / ID: 6j7i
TitleFusion protein of heme oxygenase-1 and NADPH cytochrome P450 reductase (15aa)
ComponentsHeme oxygenase 1,NADPH--cytochrome P450 reductase
KeywordsOXIDOREDUCTASE / fusion protein / redox complex
Function / homology
Function and homology information


iron-cytochrome-c reductase activity / Regulation of HMOX1 expression and activity / nitrate catabolic process / cellular organofluorine metabolic process / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / demethylation / response to 3-methylcholanthrene / Heme degradation / nitric oxide dioxygenase NAD(P)H activity ...iron-cytochrome-c reductase activity / Regulation of HMOX1 expression and activity / nitrate catabolic process / cellular organofluorine metabolic process / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / demethylation / response to 3-methylcholanthrene / Heme degradation / nitric oxide dioxygenase NAD(P)H activity / carnitine metabolic process / flavonoid metabolic process / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / heme metabolic process / response to arachidonic acid / nitric oxide catabolic process / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation / cytochrome-b5 reductase activity, acting on NAD(P)H / phospholipase D activity / heme oxygenase (biliverdin-producing) / positive regulation of steroid hormone biosynthetic process / cellular response to cisplatin / heme oxidation / positive regulation of chondrocyte differentiation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / negative regulation of muscle cell apoptotic process / cellular response to follicle-stimulating hormone stimulus / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of mast cell cytokine production / heme catabolic process / positive regulation of cholesterol biosynthetic process / cellular response to nutrient / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / positive regulation of smoothened signaling pathway / regulation of cholesterol metabolic process / erythrocyte homeostasis / positive regulation of epithelial cell apoptotic process / cellular response to peptide hormone stimulus / epithelial cell apoptotic process / negative regulation of macroautophagy / small GTPase-mediated signal transduction / positive regulation of cell migration involved in sprouting angiogenesis / response to dexamethasone / fatty acid oxidation / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / electron transport chain / phospholipid metabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cadmium ion / response to hormone / response to nutrient / response to nicotine / liver regeneration / caveola / negative regulation of smooth muscle cell proliferation / macroautophagy / positive regulation of smooth muscle cell proliferation / response to hydrogen peroxide / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / FMN binding / flavin adenine dinucleotide binding / cellular response to heat / NADP binding / cellular response to hypoxia / angiogenesis / response to oxidative stress / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / electron transfer activity / response to hypoxia / oxidoreductase activity / hydrolase activity / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / endoplasmic reticulum / protein homodimerization activity / identical protein binding / metal ion binding / nucleus
Similarity search - Function
NADPH-cytochrome P450 reductase / Haem oxygenase conserved site / Heme oxygenase signature. / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Haem oxygenase-like, multi-helical / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain ...NADPH-cytochrome P450 reductase / Haem oxygenase conserved site / Heme oxygenase signature. / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Haem oxygenase-like, multi-helical / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / NADPH--cytochrome P450 reductase / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSugishima, M. / Sato, H. / Wada, K. / Yamamoto, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K07280 Japan
Japan Society for the Promotion of Science25840026 Japan
CitationJournal: Febs Lett. / Year: 2019
Title: Crystal structure of a NADPH-cytochrome P450 oxidoreductase (CYPOR) and heme oxygenase 1 fusion protein implies a conformational change in CYPOR upon NADPH/NADP+binding.
Authors: Sugishima, M. / Sato, H. / Wada, K. / Yamamoto, K.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme oxygenase 1,NADPH--cytochrome P450 reductase
B: Heme oxygenase 1,NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,9498
Polymers199,2332
Non-polymers3,7176
Water0
1
A: Heme oxygenase 1,NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4754
Polymers99,6161
Non-polymers1,8583
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-16 kcal/mol
Surface area35490 Å2
MethodPISA
2
B: Heme oxygenase 1,NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4754
Polymers99,6161
Non-polymers1,8583
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-16 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.771, 158.101, 188.515
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heme oxygenase 1,NADPH--cytochrome P450 reductase / HO-1 / HSP32 / P450R


Mass: 99616.344 Da / Num. of mol.: 2 / Mutation: T222P, P230A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hmox1, Por / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P06762, UniProt: P00388, heme oxygenase (biliverdin-producing), NADPH-hemoprotein reductase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P

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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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 20000, MES-NaOH, ethyl acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 35507 / % possible obs: 91.6 % / Redundancy: 3.3 % / Rsym value: 0.108 / Net I/σ(I): 8.2
Reflection shellResolution: 3.3→3.36 Å / Mean I/σ(I) obs: 1.97 / Num. unique obs: 1673 / CC1/2: 0.707 / Rsym value: 0.715 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J79

6j79


Resolution: 3.3→40.037 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.42
RfactorNum. reflection% reflection
Rfree0.2406 1973 5.81 %
Rwork0.1924 --
obs0.1952 33957 89.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→40.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13075 0 254 0 13329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313678
X-RAY DIFFRACTIONf_angle_d0.72718581
X-RAY DIFFRACTIONf_dihedral_angle_d15.1788079
X-RAY DIFFRACTIONf_chiral_restr0.0421951
X-RAY DIFFRACTIONf_plane_restr0.0052387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.38250.29941090.23091770X-RAY DIFFRACTION71
3.3825-3.47390.25971240.24191995X-RAY DIFFRACTION79
3.4739-3.57610.3181310.24922127X-RAY DIFFRACTION84
3.5761-3.69140.30761320.22852152X-RAY DIFFRACTION86
3.6914-3.82330.2851350.2052194X-RAY DIFFRACTION87
3.8233-3.97620.26181350.20582180X-RAY DIFFRACTION86
3.9762-4.1570.25061360.19342223X-RAY DIFFRACTION87
4.157-4.37590.21711420.18312282X-RAY DIFFRACTION90
4.3759-4.64970.20851460.16122366X-RAY DIFFRACTION93
4.6497-5.00810.2231530.15912478X-RAY DIFFRACTION97
5.0081-5.51090.21261560.17992533X-RAY DIFFRACTION99
5.5109-6.30570.23211580.20312554X-RAY DIFFRACTION98
6.3057-7.93430.2431560.19562543X-RAY DIFFRACTION98
7.9343-40.03950.19981600.17032587X-RAY DIFFRACTION95
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)
13.3348-0.01950.20733.9013-0.45282.4912-0.0513-0.02230.17660.01950.0218-0.1065-0.1235-0.05740.01680.28440.0594-0.09680.1809-0.02890.1674-29.687515.3488-31.7702
21.6449-1.0826-0.55291.20620.37632.36660.22120.31310.4034-0.5153-0.0595-0.4431-0.38850.6559-0.17710.5114-0.06410.02250.5641-0.02630.5907-9.836614.0407-55.5755
31.9850.8183-0.18481.49790.04882.04720.12580.08020.06950.190.1564-0.52620.02310.8831-0.14420.36150.0892-0.15110.7653-0.12680.61475.51892.8674-28.4235
42.72470.69331.1762.39750.32942.95260.18220.0161-0.53450.15290.129-0.10490.60990.4517-0.29680.57090.0906-0.14510.31640.02110.3769-18.8969-19.8401-29.5086
53.0665-0.2042-0.62744.128-0.61673.036-0.02920.0015-0.0556-0.10110.0685-0.11410.2478-0.0099-0.02840.2963-0.0478-0.07540.1566-0.01170.1663-38.2028-28.6373-65.852
64.30670.36330.63380.8302-0.79271.90230.2675-0.1271-0.09640.2028-0.337-0.51310.31340.7250.07250.64340.1248-0.13190.461-0.01950.6348-10.459-29.1502-53.3624
70.53950.90640.64953.34932.80898.25930.36430.2662-0.4672-0.5078-0.0227-0.73470.62971.493-0.49810.83790.24250.09190.86310.13550.95991.523-26.6742-71.3293
83.1226-0.82960.25371.3681-0.19881.65940.07120.4347-0.1202-0.3941-0.2097-0.50740.31840.71550.09660.60280.17380.17710.70510.1250.5175-10.2058-15.1368-86.3166
92.4911-0.6288-0.17143.18720.1976.87380.07480.11990.4212-0.2427-0.0556-0.1669-0.58450.4945-0.03430.4010.0124-0.01050.21030.03210.3759-29.03136.3667-72.7266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 192 )
2X-RAY DIFFRACTION2chain 'A' and (resid 193 through 390 )
3X-RAY DIFFRACTION3chain 'A' and (resid 391 through 727 )
4X-RAY DIFFRACTION4chain 'A' and (resid 728 through 853 )
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 192 )
6X-RAY DIFFRACTION6chain 'B' and (resid 193 through 374 )
7X-RAY DIFFRACTION7chain 'B' and (resid 375 through 429 )
8X-RAY DIFFRACTION8chain 'B' and (resid 430 through 727 )
9X-RAY DIFFRACTION9chain 'B' and (resid 728 through 853 )

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