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Yorodumi- SASDDR3: Yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex from Sachar... -
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-Basic information
Entry | Database: SASBDB / ID: SASDDR3 |
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Sample | Yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex from Sacharomyces cerevisiae
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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 / endocytic recycling / S-adenosyl-L-methionine binding / enzyme regulator activity / cytoplasmic translation / endosome / tRNA binding / cytoplasm / cytosol Similarity search - Function |
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
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. |
Contact author |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDDR3 |
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-Related structure data
-External links
Related items in Molecule of the Month |
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-Models
Model #1789 | Type: dummy / Radius of dummy atoms: 4.25 A / Symmetry: P1 / Chi-square value: 1.917 / P-value: 0.034809 Search similar-shape structures of this assembly by Omokage search (details) |
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Model #1790 | Type: mix / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 2.18 / P-value: 0.000008 Search similar-shape structures of this assembly by Omokage search (details) |
-Sample
Sample | Name: Yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex from Sacharomyces cerevisiae Specimen concentration: 0.47-3.10 / Entity id: 978 / 979 |
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Buffer | Name: 50 mM HEPES, 200 mM KCl, 5% v/v Glycerol, 10mM β-mercaptoethanol pH: 8 |
Entity #978 | Name: Trm7_yeast / Type: protein Description: Trm7: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase Formula weight: 36.494 / Num. of mol.: 1 Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) References: UniProt: P38238 Sequence: MGKSSKDKRD LYYRKAKEQG YRARSAFKLL QLNDQFHFLD DPNLKRVVDL CAAPGSWSQV LSRKLFDESP SSDKEDRKIV SVDLQPMSPI PHVTTLQADI THPKTLARIL KLFGNEKADF VCSDGAPDVT GLHDLDEYVQ QQLIMSALQL TACILKKGGT FVAKIFRGRD ...Sequence: MGKSSKDKRD LYYRKAKEQG YRARSAFKLL QLNDQFHFLD DPNLKRVVDL CAAPGSWSQV LSRKLFDESP SSDKEDRKIV SVDLQPMSPI PHVTTLQADI THPKTLARIL KLFGNEKADF VCSDGAPDVT GLHDLDEYVQ QQLIMSALQL TACILKKGGT FVAKIFRGRD IDMLYSQLGY LFDKIVCAKP RSSRGTSLEA FIVCLGYNPP SNWTPKLDVN TSVDEFFQGC FLNKLCISDK LSHWNEEERN IAEFMACGSL QSFDSDATYH DLPSSVAGTS SSLDPVQSPT NPPYKKALEL KRSGKLTRSV LEVLFQGPSH HHHHH |
Entity #979 | Name: Trm734 (WDR6_yeast) / Type: protein Description: Trm734: Regulator of Ty1 transposition protein 10 Formula weight: 116.254 / Num. of mol.: 1 Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) References: UniProt: Q08924 Sequence: MKDLSHYGPA LCVKFYNDYV LAGYGPFIHV YDYHSATLIN KCRLFHYNKV HGLSLSSEGK ILAYGARSVT IVELEDVLKK ESLVDFERIN SDWITGATFS FDNLQIYLLT CYNKVLICDL NCEVLFRKSL GGERSILYSG IIKVFGPDKV YVNAGTVMGG VIIWDLFSET ...Sequence: MKDLSHYGPA LCVKFYNDYV LAGYGPFIHV YDYHSATLIN KCRLFHYNKV HGLSLSSEGK ILAYGARSVT IVELEDVLKK ESLVDFERIN SDWITGATFS FDNLQIYLLT CYNKVLICDL NCEVLFRKSL GGERSILYSG IIKVFGPDKV YVNAGTVMGG VIIWDLFSET KIHNLLGHEG SIFYVNLSNN GRYVASCSDD RSIRLWDLET GKQLSVGWSH TARIWNLMFF DNDSKLISVS EDCTCRVWNI IESRENVAEL SISNVYEVHL IKSIWGVDVK DDEMIAVTSG NDGRLKLIDL LQLKRHGDEE TSFSLDDIAK QCGDIFEKNE SIKGFQWFSF GVIAITSLGK ILKYSDVTKQ WKLLLTNEKF NSYPITNGIQ TQNIAVFSNN KSDILLIKFS KDSADIIETE EFHLDELSKT NNCLVTEYDD DSFLLTLQSP NPREKFVCLE ISLQNLKIKS KHCFNKPENF SSSCLTSFRN HILVGSRFST LVIYNLLDES EEPFIIRRLS PGDTTTSIEF VEDKDNSAVF SVTNRDGYYV FIELTKNSLE EGPYRLSYKV LHSNKMMKGF LEGAFFNSKG EYITYGFKSS LFYLYNETNC YELASEVCGG SHRLWNLAKI TDGHVLMYIK ASRFHLRKIY NSIVPETLEN GVHGREIRDI SICPVSNTNT NDNFKDGHIF CTASEDTTIK LGYFNNRTGK VQNFWTQRKH VSGLQRCQFI NHKLMISSSA REELFLWELN DKYNKRPYMT IRQALPVSTN NSDLRIMDFD VKFISQSGDF LLVTVYSDST IKIWHYRENQ NKFDLIMQGR YKTCCLFNVV FIALKEELLV VISPTDGHLV VYNITEYVPF SVDPISGDLV DHKLDATISN LPAPVAQLPV HQSGVKSLDY VANATRTSAT ILTGGDDNGL GLSNLKLDDS NKVTLKTSDF IAAAASSTIT SGMLINGGKE VITTSVDQVI RAWEITAGKL SLVDKKRTTV ADTGSLEIIS NDEDADSEKT LLIGGVGLSI WKKLEVLFQG PSHHHHHH |
-Experimental information
Beam | Instrument name: Photon Factory (PF), High Energy Accelerator Research Organization (KEK) BL-10C City: Tsukuba / 国: Japan / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 2.05 mm | |||||||||||||||||||||||||||||||||
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Detector | Name: Pilatus3 2M / Pixsize x: 0.172 mm | |||||||||||||||||||||||||||||||||
Scan | Title: Yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex from Sacharomyces cerevisiae Measurement date: Dec 16, 2015 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 20 sec. / Number of frames: 40 / Unit: 1/A /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 592 /
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Result | Type of curve: extrapolated /
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