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- PDB-5wyr: Crystal structure and catalytic mechanism of the essential m1G37 ... -

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Basic information

Entry
Database: PDB / ID: 5wyr
TitleCrystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa
ComponentstRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase
KeywordsTRANSFERASE / tRNA (guanine-N(1)-)-methyltransferase / TrmD / Pseudomonas aerugiona
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA modification / methylation / cytoplasm
Similarity search - Function
tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases ...tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsJaroensuk, J. / Liew, C.W. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Zhong, W.H. / McBee, M.E. / Thongdee, N. / Prestwich, E.G. / DeMott, M.S. ...Jaroensuk, J. / Liew, C.W. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Zhong, W.H. / McBee, M.E. / Thongdee, N. / Prestwich, E.G. / DeMott, M.S. / Mongkolsuk, S. / Dedon, P.C. / Lescar, J. / Fuangthong, M.
CitationJournal: Rna / Year: 2019
Title: Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD fromPseudomonas aeruginosa.
Authors: Jaroensuk, J. / Wong, Y.H. / Zhong, W. / Liew, C.W. / Maenpuen, S. / Sahili, A.E. / Atichartpongkul, S. / Chionh, Y.H. / Nah, Q. / Thongdee, N. / McBee, M.E. / Prestwich, E.G. / DeMott, M.S. ...Authors: Jaroensuk, J. / Wong, Y.H. / Zhong, W. / Liew, C.W. / Maenpuen, S. / Sahili, A.E. / Atichartpongkul, S. / Chionh, Y.H. / Nah, Q. / Thongdee, N. / McBee, M.E. / Prestwich, E.G. / DeMott, M.S. / Chaiyen, P. / Mongkolsuk, S. / Dedon, P. / Lescar, J. / Fuangthong, M.
History
DepositionJan 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 2, 2019Group: Data collection / 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
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,4924
Polymers55,7292
Non-polymers7632
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-19 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.290, 85.290, 147.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-525-

HOH

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / TRNA (guanine9-N1)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 27864.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: trmD, PA14_15990 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q02RL6, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-Cl pH 8.4, 12.5% MPD, 12.5% PEG 1000, 12.5% PEG 3350, 5% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 18, 2015 / Details: Toroidal focusing
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→42.65 Å / Num. obs: 23225 / % possible obs: 99.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 60.26 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.9
Reflection shellResolution: 2.45→2.56 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2638 / % possible all: 94.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P9P

1p9p


Resolution: 2.45→40.96 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.387 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1196 5.15 %RANDOM
Rwork0.191 ---
obs0.193 23225 99.3 %-
Displacement parametersBiso mean: 59.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.459 Å20 Å20 Å2
2---0.459 Å20 Å2
3---0.9181 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.45→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 54 161 4090
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014047HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.085484HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1437SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes589HARMONIC5
X-RAY DIFFRACTIONt_it4047HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion19.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion507SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4769SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.276 120 4.55 %
Rwork0.215 2518 -
all0.218 2638 -
obs--94.59 %

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