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- PDB-4z3k: Human sepiapterin reductase in complex with the cofactor NADP+ an... -

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Basic information

Entry
Database: PDB / ID: 4z3k
TitleHuman sepiapterin reductase in complex with the cofactor NADP+ and the trypthophan metabolite xanthurenic acid
ComponentsSepiapterin reductase
KeywordsOXIDOREDUCTASE / sepiapterin-reductase / xanthurenic acid / inhibitor / tryptophan-metabolite
Function / homology
Function and homology information


sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming) / sepiapterin reductase activity / aldo-keto reductase (NADPH) activity / tetrahydrobiopterin biosynthetic process / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / NADP binding / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Sepiapterin reductase / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Xanthuric acid / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Sepiapterin reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsJohnsson, K.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Tetrahydrobiopterin Biosynthesis as a Potential Target of the Kynurenine Pathway Metabolite Xanthurenic Acid.
Authors: Haruki, H. / Hovius, R. / Pedersen, M.G. / Johnsson, K.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: Sepiapterin reductase
B: Sepiapterin reductase
C: Sepiapterin reductase
D: Sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,99819
Polymers119,5664
Non-polymers4,43315
Water2,882160
1
A: Sepiapterin reductase
C: Sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9689
Polymers59,7832
Non-polymers2,1857
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-92 kcal/mol
Surface area19750 Å2
MethodPISA
2
B: Sepiapterin reductase
D: Sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,03010
Polymers59,7832
Non-polymers2,2478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-70 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.964, 143.964, 180.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Sepiapterin reductase / / SPR


Mass: 29891.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The N-terminal MHHHHHHENLYFQGMEG is not resolved in the structure & is composed of a His_6 tag; TEV cleavage site; MEG are the 1st 3 residues of the wt protein. The C-terminal K is not visible in the structure.
Source: (gene. exp.) Homo sapiens (human) / Gene: SPR / Plasmid: pET9a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P35270, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming)

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Non-polymers , 5 types, 175 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-4KL / Xanthuric acid / Xanthurenate / 8-Hydroxykynurenic acid / 4,8-Dihydroxyquinaldic acid / Xanthurenic acid


Mass: 205.167 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H7NO4 / Comment: inhibitor, agonist*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 4.89 Å3/Da / Density % sol: 74.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% W/V PEG1000, 1.9 M Ammonium sulfate, 0.1 M Hepes pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 4, 2014
RadiationMonochromator: silicon sensor / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→124.676 Å / Num. all: 88165 / Num. obs: 88165 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 57.3 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.111 / Rsym value: 0.106 / Net I/av σ(I): 6.957 / Net I/σ(I): 20 / Num. measured all: 1136272
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.35-2.4813.31.0850.7170620128620.3071.0852.8100
2.48-2.6313.20.7111.1159900121590.2030.7114.3100
2.63-2.8112.90.4951.6147205114020.1430.4955.8100
2.81-3.0312.10.2962.6128639106420.0890.2968.9100
3.03-3.3212.20.1594.911900997910.0470.15915.5100
3.32-3.7213.50.0938.312000488690.0260.09327.6100
3.72-4.2913.30.0612.410396178240.0170.0640.4100
4.29-5.2512.90.04416.48546666300.0130.04450.8100
5.25-7.43120.04216.96184051330.0130.04246100
7.43-46.213.90.023283962828530.0060.02379.499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.56 Å46.2 Å
Translation7.56 Å46.2 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HWK

4hwk


Resolution: 2.35→124.676 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.1829 / WRfactor Rwork: 0.1541 / FOM work R set: 0.8359 / SU B: 5.614 / SU ML: 0.127 / SU R Cruickshank DPI: 0.1743 / SU Rfree: 0.1606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 4633 5.3 %RANDOM
Rwork0.1808 ---
obs0.1825 83471 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.42 Å2 / Biso mean: 50.093 Å2 / Biso min: 24.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.41 Å20 Å2
2--0.83 Å20 Å2
3----2.68 Å2
Refine analyzeLuzzati coordinate error obs: 0.301 Å
Refinement stepCycle: final / Resolution: 2.35→124.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7744 0 286 160 8190
Biso mean--42.23 43.99 -
Num. residues----1028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0198179
X-RAY DIFFRACTIONr_bond_other_d0.0020.027993
X-RAY DIFFRACTIONr_angle_refined_deg1.4462.04711118
X-RAY DIFFRACTIONr_angle_other_deg0.7323.00118371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38851032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31624.103312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.857151400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.151564
X-RAY DIFFRACTIONr_chiral_restr0.0850.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219132
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021748
X-RAY DIFFRACTIONr_mcbond_it4.4534.6734128
X-RAY DIFFRACTIONr_mcbond_other4.4514.6734127
X-RAY DIFFRACTIONr_mcangle_it6.247.0085160
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 315 -
Rwork0.281 6227 -
all-6542 -
obs--100 %

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