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- PDB-6j7a: Fusion protein of heme oxygenase-1 and NADPH cytochrome P450 redu... -

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Basic information

Entry
Database: PDB / ID: 6j7a
TitleFusion protein of heme oxygenase-1 and NADPH cytochrome P450 reductase (17aa)
ComponentsHeme oxygenase 1,NADPH--cytochrome P450 reductase
KeywordsOXIDOREDUCTASE / fusion protein / redox complex
Function / homology
Function and homology information


iron-cytochrome-c reductase activity / positive regulation of growth plate cartilage chondrocyte proliferation / arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / nitrate catabolic process / organofluorine metabolic process / Iron uptake and transport / demethylation / response to 3-methylcholanthrene / Heme degradation ...iron-cytochrome-c reductase activity / positive regulation of growth plate cartilage chondrocyte proliferation / arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / nitrate catabolic process / organofluorine metabolic process / Iron uptake and transport / demethylation / response to 3-methylcholanthrene / Heme degradation / carnitine metabolic process / flavonoid metabolic process / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / nitric oxide dioxygenase NAD(P)H activity / heme metabolic process / cellular response to gonadotropin stimulus / cytochrome-b5 reductase activity, acting on NAD(P)H / nitric oxide catabolic process / positive regulation of steroid hormone biosynthetic process / positive regulation of chondrocyte differentiation / heme oxygenase (biliverdin-producing) / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / negative regulation of muscle cell apoptotic process / wound healing involved in inflammatory response / cellular response to cisplatin / cellular response to follicle-stimulating hormone stimulus / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / cellular response to nutrient / heme catabolic process / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / positive regulation of smoothened signaling pathway / negative regulation of mast cell cytokine production / positive regulation of epithelial cell apoptotic process / phospholipase D activity / cellular response to peptide hormone stimulus / epithelial cell apoptotic process / negative regulation of ferroptosis / erythrocyte homeostasis / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of macroautophagy / small GTPase-mediated signal transduction / cellular response to cadmium ion / negative regulation of vascular associated smooth muscle cell proliferation / fatty acid oxidation / response to dexamethasone / positive regulation of macroautophagy / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / phospholipid metabolic process / response to hormone / nitric oxide biosynthetic process / response to nutrient / liver regeneration / response to nicotine / positive regulation of smooth muscle cell proliferation / macroautophagy / negative regulation of smooth muscle cell proliferation / electron transport chain / response to hydrogen peroxide / caveola / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / FMN binding / flavin adenine dinucleotide binding / NADP binding / cellular response to heat / angiogenesis / negative regulation of neuron apoptotic process / response to oxidative stress / 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 / metal ion binding / identical protein binding / nucleus / cytosol
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: 3.269 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 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 / 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)203,4908
Polymers199,7732
Non-polymers3,7176
Water543
1
A: Heme oxygenase 1,NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7454
Polymers99,8871
Non-polymers1,8583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-15 kcal/mol
Surface area35730 Å2
MethodPISA
2
B: Heme oxygenase 1,NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7454
Polymers99,8871
Non-polymers1,8583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-15 kcal/mol
Surface area35700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.686, 160.191, 188.832
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: 99886.703 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.37 Å3/Da / Density % sol: 63.46 %
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: 3.25→50 Å / Num. obs: 36941 / % possible obs: 98.3 % / Redundancy: 3.7 % / Rsym value: 0.088 / Net I/σ(I): 7.2
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 3.4 % / Num. unique obs: 1858 / CC1/2: 0.827 / Rsym value: 0.455 / % possible all: 97

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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: 3.269→46.479 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.56
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 1970 5.42 %RANDOM SELECTION
Rwork0.2278 ---
obs0.2288 36317 91.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.269→46.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13016 0 254 3 13273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213616
X-RAY DIFFRACTIONf_angle_d0.66218495
X-RAY DIFFRACTIONf_dihedral_angle_d14.5918039
X-RAY DIFFRACTIONf_chiral_restr0.041943
X-RAY DIFFRACTIONf_plane_restr0.0052374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2687-3.35040.318890.3091549X-RAY DIFFRACTION59
3.3504-3.4410.33331320.29312290X-RAY DIFFRACTION87
3.441-3.54220.31241470.2932542X-RAY DIFFRACTION97
3.5422-3.65650.31621460.30182538X-RAY DIFFRACTION97
3.6565-3.78710.28451470.26342559X-RAY DIFFRACTION97
3.7871-3.93870.25531420.26282529X-RAY DIFFRACTION95
3.9387-4.11780.27311430.25072536X-RAY DIFFRACTION96
4.1178-4.33480.22911440.2272498X-RAY DIFFRACTION94
4.3348-4.60620.23511450.20922502X-RAY DIFFRACTION94
4.6062-4.96140.22871430.18832505X-RAY DIFFRACTION95
4.9614-5.460.21971460.21292551X-RAY DIFFRACTION94
5.46-6.24850.24991500.21942577X-RAY DIFFRACTION95
6.2485-7.86620.22371490.19932592X-RAY DIFFRACTION95
7.8662-46.48350.19041470.17622579X-RAY DIFFRACTION90
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)
13.65030.29390.36915.2454-1.00442.3203-0.09370.04850.1877-0.01290.0782-0.1478-0.15770.07940.02830.29350.0473-0.08420.2401-0.04160.1943-29.524715.5831-32.0904
24.2936-1.0023-2.18540.88190.7312.70850.16210.240.4991-0.44250.099-0.3382-0.21070.4583-0.26970.5155-0.04390.00520.5081-0.02050.4966-9.993714.0214-56.1228
31.62840.7141-0.18941.74570.24521.97250.1520.0294-0.07940.28360.2474-0.70450.04750.8782-0.16660.29660.1259-0.14450.8348-0.20020.76255.5852.9958-28.9679
42.4090.56470.60661.9026-0.13453.44490.23010.0207-0.65460.23440.1625-0.16780.7340.4837-0.33910.65670.1262-0.19480.32980.01780.5109-18.8795-19.7787-29.7004
52.4327-0.2666-0.73654.0376-0.54422.5122-0.0670.0803-0.0539-0.24220.05970.05250.2085-0.05420.01010.3678-0.0126-0.15490.2539-0.02390.2256-38.4056-29.1382-65.8649
63.63861.15010.58450.825-0.28421.72850.24020.143-0.10750.1427-0.2292-0.55370.23260.67760.0190.56340.1672-0.13750.4968-0.00250.6997-8.7253-28.0551-55.6637
73.6579-0.49940.6922.20920.08141.74440.2110.4041-0.2101-0.6112-0.2713-0.66820.2550.66530.04070.82930.28860.22060.84970.14860.5769-5.6867-18.7787-87.176
81.0322-0.4673-0.3182.30531.09834.20450.10610.24860.2918-0.6221-0.0764-0.0151-0.4510.2679-0.02050.62920.0655-0.07470.36340.10380.4027-30.37182.5103-75.9278
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 392 )
3X-RAY DIFFRACTION3chain 'A' and (resid 393 through 729 )
4X-RAY DIFFRACTION4chain 'A' and (resid 730 through 855 )
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 192 )
6X-RAY DIFFRACTION6chain 'B' and (resid 193 through 411 )
7X-RAY DIFFRACTION7chain 'B' and (resid 412 through 673 )
8X-RAY DIFFRACTION8chain 'B' and (resid 674 through 855 )

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