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- PDB-7ny9: CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFER... -

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Basic information

Entry
Database: PDB / ID: 7ny9
TitleCRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR COMPOUND 38
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-UV5 / Branched-chain-amino-acid aminotransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 22, 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)87,9848
Polymers86,5812
Non-polymers1,4046
Water15,583865
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-39 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.425, 103.001, 109.432
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: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 23 - 385 / Label seq-ID: 26 - 388

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-UV5 / 3-[2,6-bis(oxidanylidene)-4-(trifluoromethyl)-5~{H}-pyrimidin-1-yl]-~{N}-methyl-2-pyridin-2-yl-imidazo[1,2-a]pyridine-7-carboxamide


Mass: 430.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H13F3N6O3 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
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 3 DAYS 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: Jul 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→48.32 Å / Num. obs: 99549 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.075 / Net I/σ(I): 17.3
Reflection shellResolution: 1.6→1.7 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 15864 / CC1/2: 0.726 / Rrim(I) all: 1.06

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSVERSION Nov 1, 2016data reduction
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ABJ

2abj


Resolution: 1.6→48.32 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.175 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0874 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 2101 2.1 %RANDOM
Rwork0.1742 ---
obs0.1749 97447 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.31 Å2 / Biso mean: 23.601 Å2 / Biso min: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å2-0 Å2-0 Å2
2--1.57 Å2-0 Å2
3---1.81 Å2
Refinement stepCycle: final / Resolution: 1.6→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 94 865 6731
Biso mean--23.33 35.88 -
Num. residues----730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136106
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175700
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.6618335
X-RAY DIFFRACTIONr_angle_other_deg1.2511.57813148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89522.593297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.204151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5371533
X-RAY DIFFRACTIONr_chiral_restr0.0580.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021365
Refine LS restraints NCS

Ens-ID: 1 / Number: 11626 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.292 153 -
Rwork0.285 7074 -
obs--99.22 %
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)
10.58680.08430.1460.30130.02540.46920.00550.0312-0.1080.0019-0.03440.00720.0872-0.14010.02890.172-0.0270.01040.0601-0.03360.0399-36.416-6.741-17.695
20.53060.1362-0.21650.2553-0.17950.5779-0.0037-0.0273-0.0210.0293-0.0278-0.0366-0.04240.05170.03150.1655-0.0034-0.01390.00530.00430.0059-11.2511.514-4.658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 386
2X-RAY DIFFRACTION2B21 - 386

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