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- PDB-2pwy: Crystal Structure of a m1A58 tRNA methyltransferase -

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Basic information

Entry
Database: PDB / ID: 2pwy
TitleCrystal Structure of a m1A58 tRNA methyltransferase
ComponentstRNA (adenine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / MTASE / ADOMET / TRMI / tRNA-m1A58
Function / homology
Function and homology information


tRNA (adenine(58)-N1)-methyltransferase activity / tRNA (adenine58-N1)-methyltransferase / tRNA (m1A) methyltransferase complex / tRNA methylation / tRNA processing
Similarity search - Function
: / Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Rossmann fold ...: / Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (adenine(58)-N(1))-methyltransferase TrmI
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBarraud, P. / Golinelli-Pimpaneau, B. / Tisne, C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of Thermus thermophilus tRNA m(1)A(58) Methyltransferase and Biophysical Characterization of Its Interaction with tRNA.
Authors: Barraud, P. / Golinelli-Pimpaneau, B. / Atmanene, C. / Sanglier, S. / Van Dorsselaer, A. / Droogmans, L. / Dardel, F. / Tisne, C.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE UNP Q8GBB2 has a conflict at residue 254, ALA to GLY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (adenine-N(1)-)-methyltransferase
B: tRNA (adenine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8767
Polymers57,8192
Non-polymers1,0575
Water7,584421
1
A: tRNA (adenine-N(1)-)-methyltransferase
B: tRNA (adenine-N(1)-)-methyltransferase
hetero molecules

A: tRNA (adenine-N(1)-)-methyltransferase
B: tRNA (adenine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,75114
Polymers115,6374
Non-polymers2,11410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.440, 96.795, 140.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: translation -X,Y,-Z+1/2 ; rotation 0,0,-1

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Components

#1: Protein tRNA (adenine-N(1)-)-methyltransferase / tRNA(m1A58)-methyltransferase / tRNA(m1A58)MTase


Mass: 28909.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: trmI / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q8GBB2, EC: 2.1.1.36
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.0 M Ammonium Sulfate, 5% isopropanol, 2 mM S-adenosylhomocysteine, 1.eq tRNAiMet, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→48.168 Å / Num. obs: 67981 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 5.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.9 / Num. measured all: 71441 / Num. unique all: 9830 / Rsym value: 0.674 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å19.94 Å
Translation2.5 Å19.94 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MxCuBEdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1I9G

1i9g


Resolution: 1.7→33.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.414 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3448 5.1 %RANDOM
Rwork0.18 ---
obs0.181 67928 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.924 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3823 0 67 421 4311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213990
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9885438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12222.515163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01615603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3241530
X-RAY DIFFRACTIONr_chiral_restr0.0790.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023034
X-RAY DIFFRACTIONr_nbd_refined0.1840.21737
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2369
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.217
X-RAY DIFFRACTIONr_mcbond_it0.6641.52560
X-RAY DIFFRACTIONr_mcangle_it1.02923950
X-RAY DIFFRACTIONr_scbond_it1.81231646
X-RAY DIFFRACTIONr_scangle_it2.8214.51488
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 265 -
Rwork0.247 4709 -
obs-4974 100 %
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)
10.9373-0.60640.09261.7478-0.20090.99480.06760.0480.0472-0.0396-0.00460.00660.02890.0629-0.063-0.02070.0320.0123-0.0359-0.0068-0.0005-13.457655.4638-14.2142
20.4006-0.05530.10870.08220.00320.27870.0003-0.00570.05220.0028-0.0201-0.01370.00180.02730.0197-0.00870.0085-0.0073-0.0154-0.002-0.00889.736933.357-14.8608
32.5998-1.5420.67954.60720.53781.35580.04970.1072-0.08330.0454-0.0802-0.0909-0.0044-0.09870.0306-0.05580.0534-0.024-0.0913-0.04470.05459.12632.1293-12.8516
40.4365-0.0043-0.07230.0623-0.14170.3377-0.00580.0034-0.037-0.0058-0.00570.00580.0314-0.03290.0115-0.00510.00270.0048-0.0174-0.0132-0.0107-12.032124.4115-16.2147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 608 - 63
2X-RAY DIFFRACTION2AA61 - 25564 - 258
3X-RAY DIFFRACTION3BB5 - 608 - 63
4X-RAY DIFFRACTION4BB61 - 25464 - 257

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