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- PDB-5lae: Crystal structure of murine N1-acetylpolyamine oxidase -

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Basic information

Entry
Database: PDB / ID: 5lae
TitleCrystal structure of murine N1-acetylpolyamine oxidase
ComponentsPeroxisomal N(1)-acetyl-spermine/spermidine oxidase,Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
KeywordsOXIDOREDUCTASE / flavin amine oxidase
Function / homology
Function and homology information


N1-acetylpolyamine oxidase / N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / PAOs oxidise polyamines to amines / positive regulation of spermidine biosynthetic process / Interconversion of polyamines / putrescine biosynthetic process / spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity / N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / spermine:oxygen oxidoreductase (spermidine-forming) activity ...N1-acetylpolyamine oxidase / N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / PAOs oxidise polyamines to amines / positive regulation of spermidine biosynthetic process / Interconversion of polyamines / putrescine biosynthetic process / spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity / N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / spermine:oxygen oxidoreductase (spermidine-forming) activity / putrescine catabolic process / polyamine oxidase activity / polyamine catabolic process / spermidine catabolic process / spermine catabolic process / Peroxisomal protein import / peroxisomal matrix
Similarity search - Function
Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSjogren, T. / Aagaard, A. / Snijder, A. / Barlind, L.
CitationJournal: Biochemistry / Year: 2017
Title: The Structure of Murine N(1)-Acetylspermine Oxidase Reveals Molecular Details of Vertebrate Polyamine Catabolism.
Authors: Sjogren, T. / Wassvik, C.M. / Snijder, A. / Aagaard, A. / Kumanomidou, T. / Barlind, L. / Kaminski, T.P. / Kashima, A. / Yokota, T. / Fjellstrom, O.
History
DepositionJun 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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: Peroxisomal N(1)-acetyl-spermine/spermidine oxidase,Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6044
Polymers54,6351
Non-polymers9703
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-10 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.975, 121.975, 55.093
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Peroxisomal N(1)-acetyl-spermine/spermidine oxidase,Peroxisomal N(1)-acetyl-spermine/spermidine oxidase / Polyamine oxidase


Mass: 54634.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence includes 3 aa N-terminal deletion and a loop deletion where 6 residues (451-457) are replaced with a single glycine residue.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Paox, Pao / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q8C0L6, N1-acetylpolyamine oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein at 23mg/ml in 20 mM HEPES, pH 7.0, 100 mM NaCl, 5% (v/v) glycerol and 2.5 mM TCEP was equilibrated against 2.2 M (NH4)2SO4, 0.2 M NaSCN, 0.1 M Tris pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2015
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.85→49 Å / Num. obs: 40245 / % possible obs: 99.2 % / Redundancy: 9.8 % / Biso Wilson estimate: 26.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.9
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / % possible all: 95

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQ5

1bq5


Resolution: 1.85→49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.134 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2038 5.08 %RANDOM
Rwork0.179 ---
obs0.181 40091 100 %-
Displacement parametersBiso mean: 31.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.6123 Å20 Å20 Å2
2--0.6123 Å20 Å2
3----1.2246 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.85→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3534 0 65 287 3886
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093687HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.965011HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1248SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes572HARMONIC5
X-RAY DIFFRACTIONt_it3687HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion16.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion468SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4468SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 149 5.08 %
Rwork0.21 2782 -
all0.212 2931 -
obs--100 %

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