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- PDB-1ohy: 4-AMINOBUTYRATE-AMINOTRANSFERASE inactivated by gamma-ethynyl GABA -

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Basic information

Entry
Database: PDB / ID: 1ohy
Title4-AMINOBUTYRATE-AMINOTRANSFERASE inactivated by gamma-ethynyl GABA
Components4-AMINOBUTYRATE AMINOTRANSFERASE
KeywordsTRANSFERASE / PLP-DEPENDENT ENZYME / AMINOTRANSFERASE / 4- AMINOBUTYRIC ACID / ANTIEPILEPTIC DRUG TARGET / VIGABATRIN PYRIDOXAL PHOSPHATE / NEUROTRANSMITTER DEGRADATION / MITOCHONDRION / TRANSIT PEPTIDE
Function / homology
Function and homology information


4-aminobutyrate transaminase complex / succinate-semialdehyde dehydrogenase binding / (S)-3-amino-2-methylpropionate transaminase activity / Degradation of GABA / (S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid catabolic process / nervous system process / 2 iron, 2 sulfur cluster binding ...4-aminobutyrate transaminase complex / succinate-semialdehyde dehydrogenase binding / (S)-3-amino-2-methylpropionate transaminase activity / Degradation of GABA / (S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid catabolic process / nervous system process / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / metal ion binding / identical protein binding / cytosol
Similarity search - Function
4-aminobutyrate aminotransferase, eukaryotic / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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, small domain ...4-aminobutyrate aminotransferase, eukaryotic / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / (4E)-4-AMINOHEX-4-ENOIC ACID / PYRIDOXAL-5'-PHOSPHATE / 4-aminobutyrate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.8 Å
AuthorsStorici, P. / Schirmer, T.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structures of {Gamma}-Aminobutyric Acid (Gaba) Aminotransferase, a Pyridoxal 5'-Phosphate, and [2Fe-2S] Cluster-Containing Enzyme, Complexed with {Gamma}-Ethynyl-Gaba and with the Antiepilepsy Drug Vigabatrin
Authors: Storici, P. / De Biase, D. / Bossa, F. / Bruno, S. / Mozzarelli, A. / Peneff, C. / Silverman, R. / Schirmer, T.
#1: Journal: Biochemistry / Year: 1999
Title: Crystal Structure of Gaba-Aminotransferase, a Target for Antiepileptic Drug Therapy
Authors: Storici, P. / Capitani, G. / De Biase, D. / Moser, M. / John, R.A. / Jansonius, J.N. / Schirmer, T.
History
DepositionJun 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: 4-AMINOBUTYRATE AMINOTRANSFERASE
B: 4-AMINOBUTYRATE AMINOTRANSFERASE
C: 4-AMINOBUTYRATE AMINOTRANSFERASE
D: 4-AMINOBUTYRATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,33314
Polymers213,4764
Non-polymers1,85710
Water5,116284
1
A: 4-AMINOBUTYRATE AMINOTRANSFERASE
B: 4-AMINOBUTYRATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6667
Polymers106,7382
Non-polymers9285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: 4-AMINOBUTYRATE AMINOTRANSFERASE
D: 4-AMINOBUTYRATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6667
Polymers106,7382
Non-polymers9285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.020, 225.881, 70.349
Angle α, β, γ (deg.)90.00, 108.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRTHRTHRAA13 - 2013 - 20
21TYRTYRTHRTHRBB13 - 2013 - 20
31TYRTYRTHRTHRCC13 - 2013 - 20
41TYRTYRTHRTHRDD13 - 2013 - 20
12VALVALGLNGLNAA22 - 3322 - 33
22VALVALGLNGLNBB22 - 3322 - 33
32VALVALGLNGLNCC22 - 3322 - 33
42VALVALGLNGLNDD22 - 3322 - 33
13GLNGLNGLUGLUAA38 - 5138 - 51
23GLNGLNGLUGLUBB38 - 5138 - 51
33GLNGLNGLUGLUCC38 - 5138 - 51
43GLNGLNGLUGLUDD38 - 5138 - 51
14ASNASNMETMETAA55 - 13355 - 133
24ASNASNMETMETBB55 - 13355 - 133
34ASNASNMETMETCC55 - 13355 - 133
44ASNASNMETMETDD55 - 13355 - 133
15ASNASNTRPTRPAA140 - 150140 - 150
25ASNASNTRPTRPBB140 - 150140 - 150
35ASNASNTRPTRPCC140 - 150140 - 150
45ASNASNTRPTRPDD140 - 150140 - 150
16SERSERPHEPHEAA162 - 220162 - 220
26SERSERPHEPHEBB162 - 220162 - 220
36SERSERPHEPHECC162 - 220162 - 220
46SERSERPHEPHEDD162 - 220162 - 220
17PHEPHELEULEUAA230 - 450230 - 450
27PHEPHELEULEUBB230 - 450230 - 450
37PHEPHELEULEUCC230 - 450230 - 450
47PHEPHELEULEUDD230 - 450230 - 450

NCS oper:
IDCodeMatrixVector
1given(-0.4209, 0.9067, -0.0277), (0.9068, 0.4199, -0.0365), (-0.0215, -0.0405, -0.9989)27.1663, -15.6312, 59.5189
2given(0.2282, 0.4667, 0.8545), (-0.9628, -0.0223, 0.2693), (0.1448, -0.8841, 0.4442)0.9499, 61.2467, 51.5983
3given(0.3109, 0.3716, -0.8748), (0.3802, -0.8922, -0.2439), (-0.8711, -0.2567, -0.4187)50.6042, 51.6075, 95.9305

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Components

#1: Protein
4-AMINOBUTYRATE AMINOTRANSFERASE / MITOCHONDRIAL PRECURSOR / GAMMA-AMINO-N-BUTYRATE TRANSAMINASE / GABA TRANSAMINASE / GABA ...MITOCHONDRIAL PRECURSOR / GAMMA-AMINO-N-BUTYRATE TRANSAMINASE / GABA TRANSAMINASE / GABA AMINOTRANSFERASE / GABA-AT / GABA-T / ABAT / GABAT


Mass: 53368.996 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: AFTER REACTION WITH 4-AMINO-5-HEXYNOIC ACID (GEG)(GAMMA-ETHYNYL GABA) THE FRAGMENT GEG HAS BEEN GENERATED WHICH IS COVALENTLY ATTACHED VIA A DOUBLE BOND TO C4A OF PLP AND VIA A SINGLE BOND ...Details: AFTER REACTION WITH 4-AMINO-5-HEXYNOIC ACID (GEG)(GAMMA-ETHYNYL GABA) THE FRAGMENT GEG HAS BEEN GENERATED WHICH IS COVALENTLY ATTACHED VIA A DOUBLE BOND TO C4A OF PLP AND VIA A SINGLE BOND TO NZ OF THE ACTIVE SITE LYS 329
Source: (natural) SUS SCROFA (pig) / Organ: LIVER
References: UniProt: P80147, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-GEG / (4E)-4-AMINOHEX-4-ENOIC ACID


Mass: 129.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO2
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: 4-AMINOBUTANOATE + 2-OXOGLUTARATE = SUCCINATE SEMIALDEHYDE + L-GLUTAMATE.
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 39 %
Crystal growpH: 5.7 / Details: pH 5.70
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-14 mg/mlprotein1drop
240 mMsodium acetate1droppH5.4
316-18 %PEG40001reservoir
40-10 %glycerol1reservoir
550 mMsodium cacodylate1reservoirpH6.0
61 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 42804 / % possible obs: 85.7 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.6199
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.47 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.44 / % possible all: 78.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. obs: 42802 / Redundancy: 2.5 % / Rmerge(I) obs: 0.098

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.884 / SU B: 16.41 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2079 4.9 %RANDOM
Rwork0.198 ---
obs-40293 84.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 9.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å2-2.12 Å2
2---0.84 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14403 0 104 284 14791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02114872
X-RAY DIFFRACTIONr_bond_other_d0.0180.0213317
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.95620115
X-RAY DIFFRACTIONr_angle_other_deg1.454330948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.93151841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.22157
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216599
X-RAY DIFFRACTIONr_gen_planes_other0.0160.023090
X-RAY DIFFRACTIONr_nbd_refined0.2190.24000
X-RAY DIFFRACTIONr_nbd_other0.2680.216700
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.28616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2531
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3570.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3210.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0191.59210
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.038214808
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.135662
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.1354.55306
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6044 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.020.1
2Btight positional0.030.1
3Ctight positional0.020.1
4Dtight positional0.030.1
1Atight thermal0.044
2Btight thermal0.034
3Ctight thermal0.044
4Dtight thermal0.044
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.341 112
Rwork0.274 2384
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)
10.8635-0.18030.0931.51490.10861.269-0.0421-0.0102-0.1140.1182-0.02530.210.1229-0.09720.06740.15120.0520.04010.098-0.05530.12385.6683.53421.259
20.7049-0.04040.36271.03930.46831.4230.0002-0.1288-0.09410.39690.055-0.05150.38920.2786-0.05520.37850.1378-0.00370.2046-0.03160.147926.843-9.49837.377
30.9478-0.12150.23970.99060.03751.01540.02090.14660.038-0.1269-0.0250.0867-0.115-0.00630.00410.0506-0.02080.00390.06550.01350.038422.01361.14258.271
41.3599-0.23490.22410.4083-0.01930.7492-0.0028-0.0661-0.04860.05430.01350.02120.05310.0385-0.01070.0139-0.00360.01820.01630.00010.025434.56845.31380.023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 471
2X-RAY DIFFRACTION2B11 - 471
3X-RAY DIFFRACTION3C11 - 471
4X-RAY DIFFRACTION4D11 - 471
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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