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

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Basic information

Entry
Database: PDB / ID: 7ntr
TitleCRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SUBSTRATE MIMIC 3-PHENYLPROPIONATE
ComponentsBranched-chain-amino-acid aminotransferase, cytosolic
KeywordsTRANSFERASE / BRANCHED-CHAIN-AMINO-ACID AMINOTRANSFERASE / CYTOSOLIC / PYRIDOXAL-PHOSPHATE-DEPENDENT AMINOTRANSFERASE
Function / homology
Function and homology information


L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / valine biosynthetic process ...L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / valine biosynthetic process / amino acid 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. / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
HYDROCINNAMIC ACID / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 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 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)87,4007
Polymers86,5812
Non-polymers8195
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-28 kcal/mol
Surface area26580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.844, 103.795, 110.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: S379R
Source method: isolated from a genetically manipulated source
Details: S379R ENGINEERED / Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT1, BCT1, ECA39 / Production host: Escherichia coli (E. coli)
References: UniProt: P54687, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-HCI / HYDROCINNAMIC ACID / 3PP / 3-PHENYLPROPIONIC ACID


Mass: 150.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O2 / 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.: 401 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
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. PREINCUBATED OVER NIGHT WITH 10 MILLIMOLAR 3-PHENYL-PROPIONATE AND 3 MILLIMOLAR DTT. DROPS MADE ...Details: PROTEIN AT 17 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.0, 100 MILLIMOLAR NACL, 3 MILLIMOLAR DTT. PREINCUBATED OVER NIGHT WITH 10 MILLIMOLAR 3-PHENYL-PROPIONATE AND 3 MILLIMOLAR DTT. DROPS MADE FROM 1 MICROLITER PROTEIN AND 1 MICROLITER RESERVOIR (225 MILLIMOLAR MGCL2, 16-20 % (W/V) PEG 3350. CRYO: RESERVOIR SOLUTION COMPLEMENTED WITH 20 % (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.21→75.5 Å / Num. obs: 39094 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.144 / Net I/σ(I): 9.86
Reflection shellResolution: 2.21→2.34 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.89 / Num. unique obs: 5999 / CC1/2: 0.719 / Rrim(I) all: 0.91 / % possible all: 96.1

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Processing

Software
NameVersionClassification
XDSMARCH 30, 2013data reduction
REFMAC5.7.0032refinement
PDB_EXTRACT3.27data extraction
XSCALEJuly 4, 2012data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ABJ

2abj


Resolution: 2.23→42.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.366 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 1900 5 %RANDOM
Rwork0.1699 ---
obs0.1735 36147 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.86 Å2 / Biso mean: 34.72 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0 Å2
2--0.87 Å2-0 Å2
3----0.85 Å2
Refinement stepCycle: final / Resolution: 2.23→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5724 0 53 402 6179
Biso mean--51.28 35.1 -
Num. residues----723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196008
X-RAY DIFFRACTIONr_bond_other_d0.0020.025667
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9758188
X-RAY DIFFRACTIONr_angle_other_deg0.866313072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10124.242264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.758151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8271532
X-RAY DIFFRACTIONr_chiral_restr0.10.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216745
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021345
LS refinement shellResolution: 2.23→2.288 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 136 -
Rwork0.24 2625 -
all-2761 -
obs--99.93 %
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)
10.95040.021-0.35290.3635-0.090.8041-0.0021-0.04150.1874-0.0178-0.0320.0246-0.12-0.1840.03410.10430.0333-0.01740.0741-0.07180.2408-36.3797.1817.654
21.0374-0.52430.36110.6399-0.32330.99870.00260.01830.0959-0.007-0.0342-0.09050.08250.08170.03170.0773-0.00380.00870.0132-0.02480.1777-11.345-11.5084.452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 385
2X-RAY DIFFRACTION2B24 - 385

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