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- PDB-2hhf: X-ray crystal structure of oxidized human mitochondrial branched ... -

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Basic information

Entry
Database: PDB / ID: 2hhf
TitleX-ray crystal structure of oxidized human mitochondrial branched chain aminotransferase (hBCATm)
Components(Branched-chain-amino-acid aminotransferase, mitochondrial) x 2
KeywordsTRANSFERASE / D-aminoacid aminotransferase-like PLP-dependent enzymes
Function / homology
Function and homology information


regulation of hormone levels / branched-chain-amino-acid transaminase activity / L-leucine-2-oxoglutarate transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / branched-chain amino acid biosynthetic process / L-isoleucine catabolic process / branched-chain-amino-acid transaminase / L-leucine biosynthetic process / Branched-chain amino acid catabolism ...regulation of hormone levels / branched-chain-amino-acid transaminase activity / L-leucine-2-oxoglutarate transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / branched-chain amino acid biosynthetic process / L-isoleucine catabolic process / branched-chain-amino-acid transaminase / L-leucine biosynthetic process / Branched-chain amino acid catabolism / L-valine biosynthetic process / cellular response to leukemia inhibitory factor / lipid metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm
Similarity search - Function
Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes ...Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYennawar, N.H. / Hutson, S.M.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Human Mitochondrial Branched Chain Aminotransferase Isozyme: STRUCTURAL ROLE OF THE CXXC CENTER IN CATALYSIS.
Authors: Yennawar, N.H. / Islam, M.M. / Conway, M. / Wallin, R. / Hutson, S.M.
#1: Journal: J.BIOL.CHEM. / Year: 1998
Title: Overexpression and characterization of the human mitochondrial and cytosolic branched-chain aminotransferases.
Authors: Davoodi, J. / Drown, P.M. / Bledsoe, R.K. / Wallin, R. / Reinhart, G.D. / Hutson, S.M.
#2: Journal: Biochim.Biophys.Acta / Year: 1997
Title: Cloning of the rat and human mitochondrial branched chain aminotransferases (BCATm).
Authors: Bledsoe, R.K. / Dawson, P.A. / Hutson, S.M.
History
DepositionJun 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Branched-chain-amino-acid aminotransferase, mitochondrial
B: Branched-chain-amino-acid aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5995
Polymers82,8662
Non-polymers7333
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-19 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.123, 104.183, 58.264
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Branched-chain-amino-acid aminotransferase, mitochondrial / BCATm / Placental protein 18 / PP18 / MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE


Mass: 41450.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: In this entity, residue 141 in chain A is a modified Tyrosine, TYO. The authors state that Tyrosine 141 has undergone radiation damage in the presence of the oxidizing agent hydrogen peroxide to form TYO.
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT2, BCATM, ECA40 / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21de3
References: UniProt: O15382, branched-chain-amino-acid transaminase
#2: Protein Branched-chain-amino-acid aminotransferase, mitochondrial / BCATm / Placental protein 18 / PP18 / MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE


Mass: 41416.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: In this entity, residue 641 is TYR. The authors state that the tyrosine of the second monomer (Chain B) is not modified.
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT2, BCATM, ECA40 / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21de3 / References: UniProt: O15382
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / 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.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Peg1500, Hepes, pH 7.0, H2O2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91609 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2002 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91609 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 63136 / Num. obs: 58070 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.077 / Χ2: 1.057 / Net I/σ(I): 9
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.483 / Num. unique all: 2757 / Χ2: 0.941 / % possible all: 86.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EKF

1ekf


Resolution: 1.8→30 Å / FOM work R set: 0.79 / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that is not the terminal residue of the sequence. In all these instances the OXT was ...Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that is not the terminal residue of the sequence. In all these instances the OXT was changed to N of the next residue.
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2886 4.6 %RANDOM
Rwork0.252 ---
obs0.283 57920 91.8 %-
all-63068 --
Solvent computationBsol: 15.948 Å2
Displacement parametersBiso mean: 24.072 Å2
Baniso -1Baniso -2Baniso -3
1-6.899 Å20 Å2-0.539 Å2
2---8.598 Å20 Å2
3---1.698 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5684 0 45 206 5935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2.066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.8-1.810.324570.31310071064
1.81-1.820.388440.31410651109
1.82-1.840.308520.30210661118
1.84-1.850.282610.29510541115
1.85-1.860.326640.29210461110
1.86-1.880.366710.30410461117
1.88-1.890.314500.30610911141
1.89-1.910.283450.28310581103
1.91-1.920.299550.28910671122
1.92-1.940.386660.29810551121
1.94-1.960.354550.28210751130
1.96-1.970.307540.27710351089
1.97-1.990.272480.28211051153
1.99-2.010.336500.27610641114
2.01-2.030.334510.27510741125
2.03-2.050.32640.26210721136
2.05-2.070.342470.27310851132
2.07-2.090.3490.27510921141
2.09-2.110.328550.25610601115
2.11-2.130.296580.2710971155
2.13-2.160.327510.2611001151
2.16-2.180.31710.26210551126
2.18-2.210.296660.26310841150
2.21-2.240.317640.24710891153
2.24-2.270.297650.25710661131
2.27-2.30.317620.26511181180
2.3-2.330.305700.26310861156
2.33-2.370.325550.2511111166
2.37-2.40.293510.27411241175
2.4-2.440.382680.28711291197
2.44-2.480.258630.25611181181
2.48-2.530.312630.24911381201
2.53-2.580.241530.26411091162
2.58-2.630.391570.26811851242
2.63-2.690.284500.26711401190
2.69-2.750.304470.25611901237
2.75-2.820.377560.26911431199
2.82-2.90.297630.25812151278
2.9-2.980.271480.24811821230
2.98-3.080.235570.24311881245
3.08-3.190.251540.24711461200
3.19-3.310.25710.23511721243
3.31-3.470.268600.23311341194
3.47-3.650.249700.24411301200
3.65-3.880.25690.23211281197
3.88-4.170.283540.23610581112
4.17-4.590.236500.22210411091
4.59-5.250.237680.2210681136
5.25-6.610.296580.24111721230
6.61-300.203560.21811011157
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3acy+glyc.par
X-RAY DIFFRACTION4epe_xplor_par.txt

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