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- PDB-2r2n: The crystal structure of human kynurenine aminotransferase II in ... -

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Basic information

Entry
Database: PDB / ID: 2r2n
TitleThe crystal structure of human kynurenine aminotransferase II in complex with kynurenine
ComponentsKynurenine/alpha-aminoadipate aminotransferase mitochondrial
KeywordsTRANSFERASE / alpha & beta protein / PLP-dependent transferase / Aminotransferase / Mitochondrion / Multifunctional enzyme / Pyridoxal phosphate / Transit peptide
Function / homology
Function and homology information


glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / kynurenine-glyoxylate transaminase / kynurenine-glyoxylate transaminase activity / 2-aminoadipate transaminase activity / alpha-amino acid metabolic process / kynurenine-oxoglutarate transaminase ...glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / kynurenine-glyoxylate transaminase / kynurenine-glyoxylate transaminase activity / 2-aminoadipate transaminase activity / alpha-amino acid metabolic process / kynurenine-oxoglutarate transaminase / L-lysine catabolic process to acetyl-CoA via saccharopine / kynurenine-oxoglutarate transaminase activity / Lysine catabolism / kynurenine metabolic process / glutamate metabolic process / Tryptophan catabolism / 2-oxoglutarate metabolic process / biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity / mitochondrion
Similarity search - Function
: / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...: / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHan, Q. / Robinson, H. / Li, J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of human kynurenine aminotransferase II.
Authors: Han, Q. / Robinson, H. / Li, J.
History
DepositionAug 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kynurenine/alpha-aminoadipate aminotransferase mitochondrial
B: Kynurenine/alpha-aminoadipate aminotransferase mitochondrial
C: Kynurenine/alpha-aminoadipate aminotransferase mitochondrial
D: Kynurenine/alpha-aminoadipate aminotransferase mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,98018
Polymers189,6024
Non-polymers2,37814
Water24,1581341
1
A: Kynurenine/alpha-aminoadipate aminotransferase mitochondrial
B: Kynurenine/alpha-aminoadipate aminotransferase mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8067
Polymers94,8012
Non-polymers1,0055
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
MethodPISA
2
C: Kynurenine/alpha-aminoadipate aminotransferase mitochondrial
D: Kynurenine/alpha-aminoadipate aminotransferase mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,17411
Polymers94,8012
Non-polymers1,3739
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.843, 109.360, 119.354
Angle α, β, γ (deg.)90.00, 94.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Kynurenine/alpha-aminoadipate aminotransferase mitochondrial / KAT/AadAT / Kynurenine--oxoglutarate transaminase II / Kynurenine aminotransferase II / Kynurenine-- ...KAT/AadAT / Kynurenine--oxoglutarate transaminase II / Kynurenine aminotransferase II / Kynurenine--oxoglutarate aminotransferase II / 2-aminoadipate transaminase / 2- aminoadipate aminotransferase / Alpha-aminoadipate aminotransferase / AadAT


Mass: 47400.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AADAT, KAT2 / Plasmid: PTYB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q8N5Z0, kynurenine-oxoglutarate transaminase, 2-aminoadipate transaminase
#2: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical
ChemComp-KYN / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / L-KYNURENINE


Type: L-peptide linking / Mass: 208.214 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1341 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Hepes, 15% PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2007
RadiationMonochromator: SI 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 132070 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.373 / % possible all: 62.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qlr

2qlr


Resolution: 1.95→26.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 6185 5 %RANDOM
Rwork0.19425 ---
obs0.19568 116774 93.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.617 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→26.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13330 0 160 1341 14831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02213812
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.98418742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.67651696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65824.583576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.237152364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4841564
X-RAY DIFFRACTIONr_chiral_restr0.2070.22064
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210440
X-RAY DIFFRACTIONr_nbd_refined0.2310.27209
X-RAY DIFFRACTIONr_nbtor_refined0.3120.29437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.21282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.227
X-RAY DIFFRACTIONr_mcbond_it0.9581.58538
X-RAY DIFFRACTIONr_mcangle_it1.71213856
X-RAY DIFFRACTIONr_scbond_it2.82735274
X-RAY DIFFRACTIONr_scangle_it4.34.54886
LS refinement shellResolution: 1.949→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 307 -
Rwork0.228 5436 -
obs--59.53 %

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