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Yorodumi- PDB-6jp6: The X-ray structure of yeast tRNA methyltransferase complex of Tr... -
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-Basic information
Entry | Database: PDB / ID: 6jp6 | |||||||||
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Title | The X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential for 2'-O-methylation at the first position of anticodon in specific tRNAs | |||||||||
Components |
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Keywords | TRANSFERASE / 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 / tRNA (guanine(34)-2'-O)-methyltransferase activity / tRNA (guanine) methyltransferase activity / RND1 GTPase cycle / RND2 GTPase cycle / tRNA nucleoside ribose methylation / RHOV GTPase cycle ...tRNA (cytidine32/guanosine34-2'-O)-methyltransferase / wobble position ribose methylation / tRNA 2'-O-methyltransferase activity / tRNA (cytidine(32)-2'-O)-methyltransferase activity / tRNA (guanine(34)-2'-O)-methyltransferase activity / tRNA (guanine) methyltransferase activity / RND1 GTPase cycle / RND2 GTPase cycle / tRNA nucleoside ribose methylation / RHOV GTPase cycle / RHOU GTPase cycle / tRNA methyltransferase activity / tRNA methylation / S-adenosyl-L-methionine binding / endocytic recycling / enzyme regulator activity / tRNA binding / cytoplasmic translation / endosome / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.699 Å | |||||||||
Authors | Hirata, A. / Okada, K. / Yoshii, K. / Shiraisi, H. / Saijo, S. / Yonezawa, K. / Sihimzu, N. / Hori, H. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nucleic Acids Res / Year: 2019 Title: Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition. Authors: Akira Hirata / Keisuke Okada / Kazuaki Yoshii / Hiroyuki Shiraishi / Shinya Saijo / Kento Yonezawa / Nobutaka Shimizu / Hiroyuki Hori / Abstract: The complex between Trm7 and Trm734 (Trm7-Trm734) from Saccharomyces cerevisiae catalyzes 2'-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7-Trm734 ...The complex between Trm7 and Trm734 (Trm7-Trm734) from Saccharomyces cerevisiae catalyzes 2'-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7-Trm734 complex. Purified recombinant Trm7-Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7-Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7-Trm734. Small angle X-ray scattering reveals that Trm7-Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 β-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7-Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jp6.cif.gz | 500.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jp6.ent.gz | 402 KB | Display | PDB format |
PDBx/mmJSON format | 6jp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jp6_validation.pdf.gz | 496.8 KB | Display | wwPDB validaton report |
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Full document | 6jp6_full_validation.pdf.gz | 548.8 KB | Display | |
Data in XML | 6jp6_validation.xml.gz | 89 KB | Display | |
Data in CIF | 6jp6_validation.cif.gz | 121.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/6jp6 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/6jp6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | 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 | 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 #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG400, HEPES-NaOH, ammonium sulfate, phenol, ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.699→36.433 Å / Num. obs: 100973 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 44.62 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.7→2.75 Å / Rmerge(I) obs: 0.465 / Num. unique obs: 4959 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.699→36.433 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.04 Å2 / Biso mean: 46.5571 Å2 / Biso min: 17.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.699→36.433 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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