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- PDB-3uzo: Crystal Structures of Branched-Chain Aminotransferase from Deinoc... -

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Basic information

Entry
Database: PDB / ID: 3uzo
TitleCrystal Structures of Branched-Chain Aminotransferase from Deinococcus radiodurans Complexes with alpha-Ketoisocaproate and L-Glutamate Suggest Its Radio-Resistance for Catalysis
ComponentsBranched-chain-amino-acid aminotransferase
KeywordsTRANSFERASE / BCAT / Amino-acid biosynthesis / Aminotransferase / Branched-chain amino acid biosynthesis / Pyridoxal phosphate / L-Glutamate
Function / homology
Function and homology information


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 transaminase / L-leucine biosynthetic process / L-valine biosynthetic process / isoleucine biosynthetic process
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
GLUTAMIC ACID / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, C.D. / Huang, Y.C. / Chuankhayan, P. / Hsieh, Y.C. / Huang, T.F. / Lin, C.H. / Guan, H.H. / Liu, M.Y. / Chang, W.C. / Chen, C.J.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Crystal Structures of Complexes of the Branched-Chain Aminotransferase from Deinococcus radiodurans with alpha-Ketoisocaproate and L-Glutamate Suggest the Radiation Resistance of This Enzyme for Catalysis
Authors: Chen, C.D. / Lin, C.H. / Chuankhayan, P. / Huang, Y.C. / Hsieh, Y.C. / Huang, T.F. / Guan, H.H. / Liu, M.Y. / Chang, W.C. / Chen, C.J.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Branched-chain-amino-acid aminotransferase
B: Branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7196
Polymers78,9312
Non-polymers7894
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-29 kcal/mol
Surface area23740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.881, 75.980, 79.123
Angle α, β, γ (deg.)90.00, 105.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Branched-chain-amino-acid aminotransferase


Mass: 39465.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR_1626 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RTX5, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2M Na Chloride, 25%(w/v) polyethylene glycol 3350, 0.1M Bis-Tris, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 53244 / Num. obs: 42767 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 25.09 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.06 / Net I/σ(I): 26.7
Reflection shellResolution: 2→2.09 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8.61 / Num. unique all: 5291 / Rsym value: 0.201 / % possible all: 99.2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2COJ

2coj


Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 -RANDOM
Rwork0.221 --
obs0.221 42767 -
all-53244 -
Displacement parametersBiso mean: 24.9072 Å2
Baniso -1Baniso -2Baniso -3
1-0.623 Å20 Å21.612 Å2
2--3.285 Å20 Å2
3----3.908 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 50 156 5416
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.201
RfactorNum. reflection% reflection
Rfree0.263 5291 -
Rwork0.221 --
obs-5291 99.2 %

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