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- PDB-6j79: Fusion protein of heme oxygenase-1 and NADPH-cytochrome P450 redu... -

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Basic information

Entry
Database: PDB / ID: 6j79
TitleFusion protein of heme oxygenase-1 and NADPH-cytochrome P450 reductase (13aa)
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 / carnitine metabolic process ...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 / carnitine metabolic process / flavonoid metabolic process / Cytoprotection by HMOX1 / nitric oxide dioxygenase NAD(P)H activity / negative regulation of mast cell degranulation / response to arachidonic acid / heme metabolic process / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation / nitric oxide catabolic process / 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 / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of chondrocyte differentiation / 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 / positive regulation of cholesterol biosynthetic process / heme catabolic process / cellular response to arsenic-containing substance / cellular response to nutrient / negative regulation of epithelial cell apoptotic process / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / positive regulation of smoothened signaling pathway / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / cellular response to peptide hormone stimulus / epithelial cell apoptotic process / regulation of cholesterol metabolic process / positive regulation of cell migration involved in sprouting angiogenesis / small GTPase-mediated signal transduction / negative regulation of macroautophagy / response to dexamethasone / fatty acid oxidation / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / phospholipid metabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cadmium ion / response to nutrient / response to hormone / caveola / liver regeneration / macroautophagy / electron transport chain / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / response to nicotine / 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 / NADP binding / cellular response to heat / flavin adenine dinucleotide binding / cellular response to hypoxia / angiogenesis / intracellular iron ion homeostasis / response to oxidative stress / negative regulation of neuron apoptotic process / oxidoreductase activity / electron transfer activity / hydrolase activity / response to hypoxia / 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 / structural molecule activity / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein homodimerization activity / identical protein binding / nucleus / metal ion binding
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: 3.331 Å
AuthorsSugishima, M. / Wada, 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 17, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)202,3978
Polymers198,6802
Non-polymers3,7176
Water28816
1
A: Heme oxygenase 1,NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1984
Polymers99,3401
Non-polymers1,8583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-23 kcal/mol
Surface area35880 Å2
MethodPISA
2
B: Heme oxygenase 1,NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1984
Polymers99,3401
Non-polymers1,8583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-22 kcal/mol
Surface area36420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.360, 159.780, 189.590
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: 99340.055 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 / Plasmid: pET15b / 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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 3.27 Å3/Da / Density % sol: 62.44 %
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: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.33→50 Å / Num. obs: 37461 / % possible obs: 99 % / Redundancy: 8.06 % / CC1/2: 0.999 / Rsym value: 0.096 / Net I/σ(I): 14.04
Reflection shellResolution: 3.33→3.42 Å / Redundancy: 7.57 % / Num. unique obs: 2499 / CC1/2: 0.811 / Rsym value: 1.183 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WKT

3wkt


Resolution: 3.331→43.674 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 1872 5 %Random selection
Rwork0.2019 ---
obs0.2042 37446 99.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.331→43.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13075 0 254 16 13345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213677
X-RAY DIFFRACTIONf_angle_d0.64118582
X-RAY DIFFRACTIONf_dihedral_angle_d15.3678074
X-RAY DIFFRACTIONf_chiral_restr0.0391951
X-RAY DIFFRACTIONf_plane_restr0.0042391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3313-3.42140.41631290.34882459X-RAY DIFFRACTION92
3.4214-3.5220.37961440.30222728X-RAY DIFFRACTION100
3.522-3.63560.35391440.28632739X-RAY DIFFRACTION100
3.6356-3.76550.33321420.2632703X-RAY DIFFRACTION100
3.7655-3.91620.27391440.23562726X-RAY DIFFRACTION100
3.9162-4.09430.2981430.22782720X-RAY DIFFRACTION99
4.0943-4.310.22251430.18862721X-RAY DIFFRACTION100
4.31-4.57980.22881450.16822749X-RAY DIFFRACTION100
4.5798-4.93290.20131450.16392748X-RAY DIFFRACTION100
4.9329-5.42850.24281450.18032760X-RAY DIFFRACTION100
5.4285-6.21210.241460.19842782X-RAY DIFFRACTION100
6.2121-7.81930.24231490.19762827X-RAY DIFFRACTION100
7.8193-43.67810.21231530.18212912X-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)
13.5681-0.1355-0.41424.5183-1.21133.2998-0.05350.07690.14490.14850.1799-0.09-0.08120.1105-0.10770.92110.0515-0.14580.5773-0.09380.6811.642415.5883-32.1222
24.6666-0.5544-1.87241.51981.40762.1315-0.00460.63820.3451-0.54120.2972-0.7164-0.47150.2503-0.31561.0866-0.1368-0.09570.7918-0.00331.007830.801914.8823-56.205
30.67430.303-0.27171.72290.64412.0385-0.06460.0956-0.22790.31610.292-0.8928-0.09890.8501-0.2060.94210.1213-0.28881.357-0.20221.331250.22514.9715-31.5553
42.63582.00141.99643.21561.13642.11530.2638-0.1769-0.57410.46240.1778-0.4150.66550.2331-0.3481.39680.2168-0.2030.72960.0390.970623.6693-16.1832-26.6324
53.486-0.4142-0.79124.7460.12732.9809-0.0819-0.00330.0504-0.07630.0669-0.07950.02-0.07990.01330.8727-0.001-0.11690.52880.00960.51583.1337-29.1094-66.0527
61.57180.3606-0.28630.8218-0.32880.97250.1116-0.1480.08440.0507-0.1605-0.54880.44480.53140.11921.11410.2072-0.06560.848-0.02411.29133.3789-28.7955-59.3164
72.2475-0.607-0.07712.1760.27642.78080.19370.3625-0.0065-0.6873-0.1558-0.65620.22850.8475-0.05091.20410.12390.2241.0350.12820.954131.1494-15.0994-86.5027
83.4157-0.53621.71023.74980.68927.39650.11960.20460.462-0.5614-0.0214-0.406-0.86180.4882-0.18591.1650.03830.0520.51580.06230.809412.26765.8948-73.109
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 372 )
3X-RAY DIFFRACTION3chain 'A' and (resid 373 through 669 )
4X-RAY DIFFRACTION4chain 'A' and (resid 670 through 851 )
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 192 )
6X-RAY DIFFRACTION6chain 'B' and (resid 193 through 435 )
7X-RAY DIFFRACTION7chain 'B' and (resid 436 through 725 )
8X-RAY DIFFRACTION8chain 'B' and (resid 726 through 851 )

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