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- PDB-4je5: Crystal structure of the aromatic aminotransferase Aro8, a putati... -

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Basic information

Entry
Database: PDB / ID: 4je5
TitleCrystal structure of the aromatic aminotransferase Aro8, a putative alpha-aminoadipate aminotransferase in Saccharomyces cerevisiae
Components(Aromatic/aminoadipate aminotransferase ...) x 2
KeywordsTRANSFERASE / aromatic aminotransferase / alpha-aminoadipate aminotransferase / multifunctional enzyme / PLP-dependent / pyridoxal phosphate
Function / homology
Function and homology information


Lysine catabolism / aromatic-amino-acid transaminase activity / Tryptophan catabolism / aromatic-amino-acid transaminase / L-phenylalanine-2-oxoglutarate transaminase activity / 2-aminoadipate transaminase / 2-aminoadipate transaminase activity / alpha-amino acid metabolic process / aromatic amino acid metabolic process / aromatic amino acid family catabolic process ...Lysine catabolism / aromatic-amino-acid transaminase activity / Tryptophan catabolism / aromatic-amino-acid transaminase / L-phenylalanine-2-oxoglutarate transaminase activity / 2-aminoadipate transaminase / 2-aminoadipate transaminase activity / alpha-amino acid metabolic process / aromatic amino acid metabolic process / aromatic amino acid family catabolic process / tyrosine biosynthetic process / lysine biosynthetic process via aminoadipic acid / L-phenylalanine biosynthetic process / L-methionine salvage from methylthioadenosine / transaminase activity / aromatic amino acid family biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Aromatic/aminoadipate aminotransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.909 Å
AuthorsBulfer, S.L. / Brunzelle, J.S. / Trievel, R.C.
CitationJournal: Protein Sci. / Year: 2013
Title: Crystal structure of Saccharomyces cerevisiae Aro8, a putative alpha-aminoadipate aminotransferase.
Authors: Bulfer, S.L. / Brunzelle, J.S. / Trievel, R.C.
History
DepositionFeb 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aromatic/aminoadipate aminotransferase 1
B: Aromatic/aminoadipate aminotransferase 1
C: Aromatic/aminoadipate aminotransferase 1
D: Aromatic/aminoadipate aminotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,43112
Polymers226,4964
Non-polymers1,9358
Water18,2491013
1
A: Aromatic/aminoadipate aminotransferase 1
B: Aromatic/aminoadipate aminotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3447
Polymers113,1342
Non-polymers1,2105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-44 kcal/mol
Surface area36550 Å2
MethodPISA
2
C: Aromatic/aminoadipate aminotransferase 1
D: Aromatic/aminoadipate aminotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0875
Polymers113,3622
Non-polymers7253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-53 kcal/mol
Surface area36190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.442, 159.831, 70.642
Angle α, β, γ (deg.)90.00, 106.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Aromatic/aminoadipate aminotransferase ... , 2 types, 4 molecules ABCD

#1: Protein Aromatic/aminoadipate aminotransferase 1 / 2-aminoadipate aminotransferase / 2-aminoadipate transaminase / Alpha-aminoadipate aminotransferase ...2-aminoadipate aminotransferase / 2-aminoadipate transaminase / Alpha-aminoadipate aminotransferase / AadAT / Aromatic amino acid aminotransferase 1 / Aromatic amino acid aminotransferase I / Aromatic amino acid-requiring protein 8


Mass: 56566.988 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ARO8, YGL202W / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P53090, 2-aminoadipate transaminase, aromatic-amino-acid transaminase
#2: Protein Aromatic/aminoadipate aminotransferase 1 / 2-aminoadipate aminotransferase / 2-aminoadipate transaminase / Alpha-aminoadipate aminotransferase ...2-aminoadipate aminotransferase / 2-aminoadipate transaminase / Alpha-aminoadipate aminotransferase / AadAT / Aromatic amino acid aminotransferase 1 / Aromatic amino acid aminotransferase I / Aromatic amino acid-requiring protein 8


Mass: 56795.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ARO8, YGL202W / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P53090, 2-aminoadipate transaminase, aromatic-amino-acid transaminase

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Non-polymers , 4 types, 1021 molecules

#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1013 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: HEPES, Sodium Citrate, pH 7.4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2009
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.909→40 Å / Num. all: 181016 / Num. obs: 181016 / % possible obs: 96.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.065 / Χ2: 1.051 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.909-1.982.70.461146151.176178.4
1.98-2.063.80.359171821.15192.5
2.06-2.154.20.269184051.129198.4
2.15-2.264.40.207186601.052199.9
2.26-2.414.60.143186430.8931100
2.41-2.594.70.106186951.0371100
2.59-2.854.70.082187361.0861100
2.85-3.274.70.053186891.0721100
3.27-4.114.50.044186711.081199.5
4.11-404.50.032187200.951198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 1.909→34.25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 7.495 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 9078 5 %RANDOM
Rwork0.1821 ---
all0.18382 180889 --
obs0.1838 180889 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 84.24 Å2 / Biso mean: 28.6448 Å2 / Biso min: 5.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0.02 Å2
2--0.15 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.909→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15337 0 122 1013 16472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02216356
X-RAY DIFFRACTIONr_angle_refined_deg1.371.97422459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80352118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14624.551712
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.725152498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6241566
X-RAY DIFFRACTIONr_chiral_restr0.0920.22455
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112746
X-RAY DIFFRACTIONr_mcbond_it0.7221.510195
X-RAY DIFFRACTIONr_mcangle_it1.296216537
X-RAY DIFFRACTIONr_scbond_it2.03336161
X-RAY DIFFRACTIONr_scangle_it3.1644.55862
LS refinement shellResolution: 1.909→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 528 -
Rwork0.408 9642 -
all-10170 -
obs--73.58 %
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)
10.42460.04230.10310.3763-0.06180.5428-0.0475-0.00410.017-0.0458-0.00250.0045-0.0530.04170.050.0478-0.032-0.00290.0334-0.00970.02573.4452-22.14467.7916
20.81940.2734-0.10890.519-0.16750.91870.0202-0.2036-0.09780.0502-0.0858-0.0645-0.02960.11650.06560.025-0.02280.00470.07490.02390.023377.189-33.325340.0318
30.75290.0229-0.23750.4338-0.02540.486-0.0152-0.1008-0.06970.0655-0.03030.03860.00980.03580.04550.02980.01850.00710.0370.00580.012967.027421.393936.2727
41.0499-0.44170.00560.55410.04550.42350.01870.0590.1683-0.0152-0.0202-0.1005-0.0320.03920.00140.03890.00910.00280.01490.01390.03488.000132.082511.0888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 499
2X-RAY DIFFRACTION2B2 - 498
3X-RAY DIFFRACTION3C2 - 499
4X-RAY DIFFRACTION4D2 - 497

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