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- PDB-3vp6: Structural characterization of Glutamic Acid Decarboxylase; insig... -

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Basic information

Entry
Database: PDB / ID: 3vp6
TitleStructural characterization of Glutamic Acid Decarboxylase; insights into the mechanism of autoinactivation
ComponentsGlutamate decarboxylase 1
KeywordsLYASE / Catalytic loop swap
Function / homology
Function and homology information


GABA synthesis / glutamate decarboxylation to succinate / MECP2 regulates transcription of genes involved in GABA signaling / glutamate decarboxylase / glutamate decarboxylase activity / gamma-aminobutyric acid biosynthetic process / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / GABA synthesis, release, reuptake and degradation / inhibitory synapse / glutamate catabolic process ...GABA synthesis / glutamate decarboxylation to succinate / MECP2 regulates transcription of genes involved in GABA signaling / glutamate decarboxylase / glutamate decarboxylase activity / gamma-aminobutyric acid biosynthetic process / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / GABA synthesis, release, reuptake and degradation / inhibitory synapse / glutamate catabolic process / vesicle membrane / presynaptic active zone / locomotory exploration behavior / social behavior / GABA-ergic synapse / axon terminus / pyridoxal phosphate binding / cell cortex / chemical synaptic transmission / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #170 / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / 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 ...Aspartate Aminotransferase, domain 1 - #170 / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / 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
4-oxo-4H-pyran-2,6-dicarboxylic acid / Glutamate decarboxylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLangendorf, C.G. / Tuck, K.L. / Key, T.L.G. / Rosado, C.J. / Wong, A.S.M. / Fenalti, G. / Buckle, A.M. / Law, R.H.P. / Whisstock, J.C.
CitationJournal: Biosci.Rep. / Year: 2013
Title: Structural characterization of the mechanism through which human glutamic acid decarboxylase auto-activates
Authors: Langendorf, C.G. / Tuck, K.L. / Key, T.L.G. / Fenalti, G. / Pike, R.N. / Rosado, C.J. / Wong, A.S.M. / Buckle, A.M. / Law, R.H.P. / Whisstock, J.C.
History
DepositionFeb 27, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate decarboxylase 1
B: Glutamate decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4126
Polymers116,8592
Non-polymers5524
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13530 Å2
ΔGint-109 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.006, 64.084, 102.646
Angle α, β, γ (deg.)90.00, 108.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutamate decarboxylase 1 / 67 kDa glutamic acid decarboxylase / GAD-67 / Glutamate decarboxylase 67 kDa isoform


Mass: 58429.711 Da / Num. of mol.: 2 / Fragment: UNP residues 90-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAD1 / Plasmid: pAS-1N / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): YRD15 / References: UniProt: Q99259, glutamate decarboxylase
#2: Chemical ChemComp-HLD / 4-oxo-4H-pyran-2,6-dicarboxylic acid


Mass: 184.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 3500, 100mM Bis-Tris, pH 6.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953638 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953638 Å / Relative weight: 1
ReflectionResolution: 2.1→97.59 Å / Num. all: 62211 / Num. obs: 62211 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.78 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.213.70.5190.4431.73324890460.2690.5190.4432.7100
2.21-2.353.70.4080.34723119985250.2130.4080.3473.9100
2.35-2.513.70.2850.2433.12967080430.1470.2850.2435.2100
2.51-2.713.70.2110.1842749674860.110.2110.187.4100
2.71-2.973.70.1390.1196.12554669290.0720.1390.11911100
2.97-3.323.70.0950.0818.72300062570.0490.0950.08115.9100
3.32-3.833.70.0650.05510.82025055390.0340.0650.05523100
3.83-4.73.60.0480.04115.21708846940.0250.0480.04128.599.9
4.7-6.643.60.0440.03816.31316936610.0230.0440.03830.899.9
6.64-54.83.40.0330.02718.2689220310.0170.0330.02734.498.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
BUSTER-TNT'BUSTER 2.10.0refinement
PDB_EXTRACT3.1data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→24.25 Å / Cor.coef. Fo:Fc: 0.9101 / Cor.coef. Fo:Fc free: 0.881 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.205 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.175 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 3148 5.06 %RANDOM
Rwork0.1971 ---
obs0.199 62171 99.92 %-
Displacement parametersBiso max: 125.68 Å2 / Biso mean: 36.8516 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.9422 Å20 Å2-4.625 Å2
2---0.1746 Å20 Å2
3---1.1169 Å2
Refine analyzeLuzzati coordinate error obs: 0.279 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7613 0 38 266 7917
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2603SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes168HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1152HARMONIC5
X-RAY DIFFRACTIONt_it7831HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1021SEMIHARMONIC5
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_contact9792SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7831HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10617HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion18.33
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2089 205 4.49 %
Rwork0.191 4364 -
all0.1918 4569 -
obs--99.92 %
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)
10.5613-0.0516-0.11691.08110.05280.658-0.0282-0.09220.02130.34310.0170.14310.0041-0.06580.01130.052-0.00130.0772-0.13760.0035-0.1076-8.48811.498529.2748
20.5660.0163-0.13710.98010.1720.6479-0.0116-0.12290.00190.18890.0453-0.234-0.00620.1972-0.0337-0.0158-0.0088-0.024-0.12060.0075-0.05714.513-0.767821.4558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A93 - 1001
2X-RAY DIFFRACTION2{ B|* }B95 - 1003

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