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- PDB-7ny2: CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFER... -

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Basic information

Entry
Database: PDB / ID: 7ny2
TitleCRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR COMPOUND 35
ComponentsBranched-chain-amino-acid aminotransferase, cytosolic
KeywordsTRANSFERASE / BRANCHED-CHAIN-AMINO-ACID AMINOTRANSFERASE / PYRIDOXAL-PHOSPHATE-DEPENDENT AMINOTRANSFERASE / SMALL MOLECULE INHIBITOR
Function / homology
Function and homology information


branched-chain-amino-acid transaminase activity / branched-chain amino acid biosynthetic process / L-leucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / : / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / L-valine biosynthetic process ...branched-chain-amino-acid transaminase activity / branched-chain amino acid biosynthetic process / L-leucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / : / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / L-valine biosynthetic process / lipid metabolic process / G1/S transition of mitotic cell cycle / mitochondrion / cytosol
Similarity search - Function
Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / 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
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Chem-UUQ / Branched-chain-amino-acid aminotransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsHillig, R.C.
CitationJournal: J.Med.Chem. / Year: 2022
Title: BAY-069, a Novel (Trifluoromethyl)pyrimidinedione-Based BCAT1/2 Inhibitor and Chemical Probe.
Authors: Gunther, J. / Hillig, R.C. / Zimmermann, K. / Kaulfuss, S. / Lemos, C. / Nguyen, D. / Rehwinkel, H. / Habgood, M. / Lechner, C. / Neuhaus, R. / Ganzer, U. / Drewes, M. / Chai, J. / Bouche, L.
History
DepositionMar 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,9747
Polymers86,5812
Non-polymers1,3935
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-40 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.459, 104.964, 110.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 23 - 386 / Label seq-ID: 26 - 389

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Branched-chain-amino-acid aminotransferase, cytosolic / BCAT(c) / Protein ECA39 / BCAT1


Mass: 43290.312 Da / Num. of mol.: 2 / Mutation: Ser379Arg, engineered
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT1, BCT1, ECA39 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P54687, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-UUQ / 4-[2,4-bis(oxidanylidene)-6-(trifluoromethyl)-1H-pyrimidin-3-yl]-2-(2-methylphenoxy)naphthalene-1-carbonitrile / 4-[2,4-bis(oxidanylidene)-6-(trifluoromethyl)-1~{H}-pyrimidin-3-yl]-2-(2-methylphenoxy)naphthalene-1-carbonitrile


Mass: 437.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H14F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PROTEIN AT 17 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.0, 100 MILLIMOLAR NACL, 3 MILLIMOLAR DTT. PROTEIN PREINCUBATED OVER NIGHT AT 293 K WITH 10 MILLIMOLAR 3-PHENYL-PROPIONATE, 3 MILLIMOLAR DTT ...Details: PROTEIN AT 17 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.0, 100 MILLIMOLAR NACL, 3 MILLIMOLAR DTT. PROTEIN PREINCUBATED OVER NIGHT AT 293 K WITH 10 MILLIMOLAR 3-PHENYL-PROPIONATE, 3 MILLIMOLAR DTT AND 1.5 MILLIMOLAR PLP. DROPS MADE FROM 1 MICROLITER PROTEIN AND 1 MICROLITER RESERVOIR (225 MILLIMOLAR MGCL2, 16-20 % (W/V) PEG 3350). INHIBITOR SOAKED INTO PREFORMED CRYSTALS FOR 1 DAY AT 10 MILLIMOLAR. CRYO: RESERVOIR SOLUTION COMPLEMENTED WITH 20 % (V/V) GLYCEROL AND 10 MILLIMOLAR INHIBITOR

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.31→47.42 Å / Num. obs: 34312 / % possible obs: 98 % / Redundancy: 5.88 % / Biso Wilson estimate: 39.2 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.075 / Net I/σ(I): 19.6
Reflection shellResolution: 2.31→2.45 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 4983 / Rrim(I) all: 0.373 / % possible all: 89.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSVERSION Jun 1, 2017data reduction
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
pointlessversion 1.10.18data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ABJ

2abj


Resolution: 2.31→47.42 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.887 / SU B: 18.834 / SU ML: 0.236 / SU R Cruickshank DPI: 0.4392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.439 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 1716 5 %RANDOM
Rwork0.2064 ---
obs0.2097 32595 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.72 Å2 / Biso mean: 32.318 Å2 / Biso min: 11.06 Å2
Baniso -1Baniso -2Baniso -3
1--6.43 Å2-0 Å2-0 Å2
2--2.61 Å2-0 Å2
3---3.82 Å2
Refinement stepCycle: final / Resolution: 2.31→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5758 0 95 335 6188
Biso mean--31.56 34.04 -
Num. residues----728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136048
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175641
X-RAY DIFFRACTIONr_angle_refined_deg1.731.6628242
X-RAY DIFFRACTIONr_angle_other_deg1.1891.57713002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1795736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20522.628293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.338151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3471532
X-RAY DIFFRACTIONr_chiral_restr0.0720.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021345
Refine LS restraints NCS

Ens-ID: 1 / Number: 10586 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.313→2.373 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 100 -
Rwork0.305 1890 -
all-1990 -
obs--78.91 %
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)
11.26910.02440.3120.74980.14930.87250.0133-0.1094-0.23480.0209-0.0072-0.11960.12340.1388-0.0060.34760.03140.02020.05730.04910.080837.426-6.89217.83
21.1088-0.2363-0.48110.75680.43961.2178-0.02390.0885-0.0484-0.0349-0.03420.0687-0.0877-0.16780.05810.3095-0.0046-0.02060.0287-0.00380.009111.2111.6914.511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 386
2X-RAY DIFFRACTION2B24 - 386

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