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- PDB-2zzk: Crystal structure of tRNA wybutosine synthesizing enzyme TYW4 -

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Basic information

Entry
Database: PDB / ID: 2zzk
TitleCrystal structure of tRNA wybutosine synthesizing enzyme TYW4
ComponentsLeucine carboxyl methyltransferase 2
KeywordsTRANSFERASE / tRNA modification
Function / homology
Function and homology information


tRNAPhe [7-(3-amino-3-carboxypropyl)wyosine37-O]-methyltransferase / tRNAPhe {7-[3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methoxycarbonyltransferase / wybutosine biosynthetic process / tRNA methyltransferase activity / tRNA methylation / tRNA modification / mitochondrion / cytoplasm
Similarity search - Function
Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / Galactose oxidase, central domain / Kelch-type beta propeller / Galactose oxidase/kelch, beta-propeller / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / 6 Propeller ...Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / Galactose oxidase, central domain / Kelch-type beta propeller / Galactose oxidase/kelch, beta-propeller / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / 6 Propeller / Neuraminidase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / tRNA wybutosine-synthesizing protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.706 Å
AuthorsSuzuki, Y. / Noma, A. / Suzuki, T. / Ishitani, R. / Nureki, O.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.
Authors: Suzuki, Y. / Noma, A. / Suzuki, T. / Ishitani, R. / Nureki, O.
History
DepositionFeb 17, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Leucine carboxyl methyltransferase 2
B: Leucine carboxyl methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,0647
Polymers158,1012
Non-polymers9635
Water59433
1
A: Leucine carboxyl methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6294
Polymers79,0511
Non-polymers5783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucine carboxyl methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4353
Polymers79,0511
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.834, 90.139, 251.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Leucine carboxyl methyltransferase 2 / TYW4 / tRNA wybutosine-synthesizing protein 4


Mass: 79050.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PPM2, TYW4, YOL141W / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus
References: UniProt: Q08282, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS CONSIDER THAT THIS DIFFERENCE MAY STEM FROM A POLYMORPHISM OF THE YEAST STRAIN OR SOME ...AUTHORS CONSIDER THAT THIS DIFFERENCE MAY STEM FROM A POLYMORPHISM OF THE YEAST STRAIN OR SOME ERROR OF THE YEAST GENOME PROJECT.

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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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM ammonium citrate (pH 7) and 20 % (w/v) PEG3,350, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 48148 / Num. obs: 48148 / % possible obs: 96.6 % / Redundancy: 6.4 % / Rsym value: 0.07 / Net I/σ(I): 30.7
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 4 / Num. unique all: 1867 / Rsym value: 0.367 / % possible all: 76.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementResolution: 2.706→42.389 Å / SU ML: 0.35 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 4815 10.05 %Random
Rwork0.2097 ---
all0.216 47919 --
obs0.216 47919 96.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.596 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso mean: 73.3 Å2
Baniso -1Baniso -2Baniso -3
1-51.4613 Å20 Å20 Å2
2---13.5957 Å20 Å2
3----37.8656 Å2
Refinement stepCycle: LAST / Resolution: 2.706→42.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10801 0 65 33 10899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411092
X-RAY DIFFRACTIONf_angle_d0.82615000
X-RAY DIFFRACTIONf_dihedral_angle_d17.6564091
X-RAY DIFFRACTIONf_chiral_restr0.0571676
X-RAY DIFFRACTIONf_plane_restr0.0031926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7062-2.7370.39251310.2996108774
2.737-2.76920.36421170.2719115779
2.7692-2.80290.35941420.2826118581
2.8029-2.83840.35751270.2669125584
2.8384-2.87580.34781370.2886130389
2.8758-2.91520.33471640.2956137993
2.9152-2.95680.42521490.2923139396
2.9568-3.00090.34651890.2879145098
3.0009-3.04780.37011660.2739142999
3.0478-3.09770.37711680.25831477100
3.0977-3.15110.35791560.2646149399
3.1511-3.20840.29411420.26451466100
3.2084-3.27010.31711730.2538147199
3.2701-3.33680.31541510.23811508100
3.3368-3.40940.30561810.21891441100
3.4094-3.48860.24391550.21451492100
3.4886-3.57580.27111910.2118145299
3.5758-3.67250.31731560.21231474100
3.6725-3.78050.29861860.20941482100
3.7805-3.90240.2651550.1894147599
3.9024-4.04180.2621560.1783148899
4.0418-4.20350.20811740.16341488100
4.2035-4.39460.19111730.16161496100
4.3946-4.6260.20021580.1558151399
4.626-4.91540.23871730.15391491100
4.9154-5.29430.20781740.1641502100
5.2943-5.82590.2611540.16731520100
5.8259-6.66610.26011680.1941547100
6.6661-8.38790.24351600.19271563100
8.3879-42.39410.2481890.191162799

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