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- PDB-6jpl: The X-ray structure of yeast tRNA methyltransferase Trm7-Trm734 i... -

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Basic information

Entry
Database: PDB / ID: 6jpl
TitleThe X-ray structure of yeast tRNA methyltransferase Trm7-Trm734 in complex with S-adenosyl-L-methionine
Components
  • tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase
  • tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734
KeywordsTRANSFERASE / tRNA methyltransferase / tRNA maturation
Function / homology
Function and homology information


tRNA (cytidine32/guanosine34-2'-O)-methyltransferase / wobble position ribose methylation / tRNA 2'-O-methyltransferase activity / tRNA (cytidine(32)-2'-O)-methyltransferase activity / RND1 GTPase cycle / tRNA nucleoside ribose methylation / RHOU GTPase cycle / RHOV GTPase cycle / tRNA methyltransferase activity / tRNA methylation ...tRNA (cytidine32/guanosine34-2'-O)-methyltransferase / wobble position ribose methylation / tRNA 2'-O-methyltransferase activity / tRNA (cytidine(32)-2'-O)-methyltransferase activity / RND1 GTPase cycle / tRNA nucleoside ribose methylation / RHOU GTPase cycle / RHOV GTPase cycle / tRNA methyltransferase activity / tRNA methylation / endocytic recycling / enzyme regulator activity / cytoplasmic translation / endosome / cytoplasm
Similarity search - Function
tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase TRM7 / Ribosomal RNA large subunit methyltransferase E / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. ...tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase TRM7 / Ribosomal RNA large subunit methyltransferase E / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase / Regulator of Ty1 transposition protein 10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsHirata, A. / Okada, K. / Yoshii, K. / Shiraisi, H. / Saijo, S. / Yonezawa, K. / Shimizu, N. / Hori, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K06975 Japan
Japan Society for the Promotion of Science16H04763 Japan
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.
Authors: Hirata, A. / Okada, K. / Yoshii, K. / Shiraishi, H. / Saijo, S. / Yonezawa, K. / Shimizu, N. / Hori, H.
History
DepositionMar 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734
B: tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase
C: tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734
D: tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,11118
Polymers305,8774
Non-polymers2,23414
Water8,305461
1
A: tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734
B: tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,0559
Polymers152,9382
Non-polymers1,1177
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-73 kcal/mol
Surface area47850 Å2
MethodPISA
2
C: tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734
D: tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,0559
Polymers152,9382
Non-polymers1,1177
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-71 kcal/mol
Surface area48140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)253.558, 110.671, 133.559
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A or chain D
21chain B or chain C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSchain A or chain DAA1 - 10131 - 1013
12ARGARGSERSERchain A or chain DDD9 - 2599 - 259
21ARGARGSERSERchain B or chain CBB9 - 2599 - 259
22METMETLYSLYSchain B or chain CCC1 - 10131 - 1013

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734


Mass: 116391.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Production host: Escherichia coli (E. coli) / References: UniProt: Q08924
#2: Protein tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase


Mass: 36546.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Production host: Escherichia coli (E. coli)
References: UniProt: P38238, tRNA (cytidine32/guanosine34-2'-O)-methyltransferase

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Non-polymers , 4 types, 475 molecules

#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, HEPES-NaOH, ammonium sulfate, phenol, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 159317 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 41.99 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 29.7
Reflection shellResolution: 2.32→2.36 Å / Rmerge(I) obs: 0.687 / Num. unique obs: 7875

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→47.413 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.46
RfactorNum. reflection% reflection
Rfree0.2351 7996 5.02 %
Rwork0.2032 --
obs0.2048 159317 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.97 Å2 / Biso mean: 50.3701 Å2 / Biso min: 23.81 Å2
Refinement stepCycle: final / Resolution: 2.32→47.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19560 0 134 461 20155
Biso mean--71.14 44.59 -
Num. residues----2458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0120078
X-RAY DIFFRACTIONf_angle_d1.2527160
X-RAY DIFFRACTIONf_chiral_restr0.073068
X-RAY DIFFRACTIONf_plane_restr0.0073424
X-RAY DIFFRACTIONf_dihedral_angle_d16.09711970
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11784X-RAY DIFFRACTION5.014TORSIONAL
12B11784X-RAY DIFFRACTION5.014TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3204-2.34670.34472480.2834944519297
2.3467-2.37430.33052760.261449915267100
2.3743-2.40330.29342440.257350275271100
2.4033-2.43370.30482480.261650445292100
2.4337-2.46570.30342720.262850255297100
2.4657-2.49950.33762540.262749835237100
2.4995-2.53520.30392760.258250415317100
2.5352-2.57310.27212680.239950345302100
2.5731-2.61330.28812470.242250365283100
2.6133-2.65610.28062620.237949985260100
2.6561-2.70190.29812650.240750745339100
2.7019-2.7510.26962260.235351075333100
2.751-2.80390.29772710.243949705241100
2.8039-2.86120.31582930.257650085301100
2.8612-2.92340.29143060.241350485354100
2.9234-2.99140.27062570.240750225279100
2.9914-3.06620.26932830.228250405323100
3.0662-3.1490.31022590.234250475306100
3.149-3.24170.27552500.22649855235100
3.2417-3.34630.24552540.216251215375100
3.3463-3.46590.22772350.208651015336100
3.4659-3.60460.22082720.195550325304100
3.6046-3.76860.22732780.191850685346100
3.7686-3.96720.23972750.190250285303100
3.9672-4.21560.18772830.174650375320100
4.2156-4.54080.18062950.150350435338100
4.5408-4.99730.16732750.144850735348100
4.9973-5.71940.19132710.170550925363100
5.7194-7.20180.23572610.198351365397100
7.2018-47.42270.19032920.19085166545899

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