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- SASDDR3: Yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex from Sachar... -

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Basic information

Entry
Database: SASBDB / ID: SASDDR3
SampleYeast tRNA Nm34 methyltransferase Trm7-Trm734 complex from Sacharomyces cerevisiae
  • Trm7: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase (protein), Trm7_yeast, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
  • Trm734: Regulator of Ty1 transposition protein 10 (protein), Trm734 (WDR6_yeast), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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
tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase / Regulator of Ty1 transposition protein 10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
CitationDate: 2019 Oct 5
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
Contact author
  • Kento Yonezawa (KEK, High Energy Accelerater Research Organization (KEK), Tsukuba, Japan)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)
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)

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Sample

SampleName: Yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex from Sacharomyces cerevisiae
Specimen concentration: 0.47-3.10 / Entity id: 978 / 979
BufferName: 50 mM HEPES, 200 mM KCl, 5% v/v Glycerol, 10mM β-mercaptoethanol
pH: 8
Entity #978Name: 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 #979Name: 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

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Experimental information

BeamInstrument name: Photon Factory (PF), High Energy Accelerator Research Organization (KEK) BL-10C
City: Tsukuba / 国: Japan / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 2.05 mm
DetectorName: 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 /
MinMax
Q0.0063 0.4099
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 592 /
MinMax
Q0.0126498 0.323829
P(R) point1 592
R0 129.9
Result
Type of curve: extrapolated /
ExperimentalPorod
MW158.819 kDa136.25 kDa
Volume-218 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.1921 0.0001 0.192981 0.0001
Radius of gyration, Rg3.77 nm0.003 3.79 nm0.003

MinMax
D-12.99
Guinier point7 54

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