Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (guanosine(18)-2′-O)-methyltransferase
Synonym: SpoU
GI: 55980096
Orf: TTHA0127
COG: COG0566
UniProt: Q9FAC4
Structures: | 1V2X |
Enzyme type: methyltransferase
Position of modification - modification: t:18 - Gm


PDB Structures:


1V2X

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 A resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2'-OH group for methylation.

Download RCSB-PDB Structures:

Pdb Files   1V2X.pdb  
Pdbx/mmCIF Files   1V2X.cif  


Protein sequence:

MRERTEARRRRIEEVLRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPTFNETSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGAEKWGVSEEALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQRQRLKAGLYDRPRLDPELYQKVLADWLRK

Comments:

T. thermophilus TrmH is a Class IV AdoMet-dependent methyltransferase.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:Gm tRNA (t) all/all/eukaryotic cytosol 18 23867454   
G:Gm RNA tRNA 18 CGC-1 CGC-1 tRNAAlaCGC-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GGC-1 GGC-1 tRNAAlaGGC-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TGC-1 TGC-1 tRNAAlaTGC-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 ACG-1 ACG-1 tRNAArgACG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CCG-1 CCG-1 tRNAArgCCG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CCT-1 CCT-1 tRNAArgCCT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TCT-1 TCT-1 tRNAArgTCT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GTT-1 GTT-1 tRNAAsnGTT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GTC-1 GTC-1 tRNAAspGTC-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GCA-1 GCA-1 tRNACysGCA-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CTG-1 CTG-1 tRNAGlnCTG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TTG-1 TTG-1 tRNAGlnTTG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CTC-1 CTC-1 tRNAGluCTC-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CTC-2 CTC-2 tRNAGluCTC-2 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TTC-1 TTC-1 tRNAGluTTC-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CCC-1 CCC-1 tRNAGlyCCC-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GCC-1 GCC-1 tRNAGlyGCC-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GTG-1 GTG-1 tRNAHisGTG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GAT-1 GAT-1 tRNAIleGAT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CAT-1 CAT-1 tRNAIle2CAT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CAA-1 CAA-1 tRNALeuCAA-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CAG-1 CAG-1 tRNALeuCAG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GAG-1 GAG-1 tRNALeuGAG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TAA-1 TAA-1 tRNALeuTAA-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TAG-1 TAG-1 tRNALeuTAG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CTT-1 CTT-1 tRNALysCTT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TTT-1 TTT-1 tRNALysTTT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CAT-1 CAT-1 tRNAMetCAT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CAT-2 CAT-2 tRNAMetCAT-2 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GAA-1 GAA-1 tRNAPheGAA-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CGG-1 CGG-1 tRNAProCGG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GGG-1 GGG-1 tRNAProGGG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TGG-1 TGG-1 tRNAProTGG-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CGA-1 CGA-1 tRNASerCGA-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GCT-1 GCT-1 tRNASerGCT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GGA-1 GGA-1 tRNASerGGA-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TGA-1 TGA-1 tRNASerTGA-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CGT-1 CGT-1 tRNAThrCGT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GGT-1 GGT-1 tRNAThrGGT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TGT-1 TGT-1 tRNAThrTGT-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CCA-1 CCA-1 tRNATrpCCA-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GTA-1 GTA-1 tRNATyrGTA-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 CAC-1 CAC-1 tRNAValCAC-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 GAC-1 GAC-1 tRNAValGAC-1 D-stem loop Prokaryotic Cytosol 23867454   
G:Gm RNA tRNA 18 TAC-1 TAC-1 tRNAValTAC-1 D-stem loop Prokaryotic Cytosol 23867454   



Publications:

Title Authors Journal Details PubMed Id DOI
Identification and characterization of tRNA (Gm18) methyltransferase from Thermus thermophilus HB8: domain structure and conserved amino acid sequence motifs. Hori H, Suzuki T, Sugawara K, Inoue Y, Shibata T, Kuramitsu S, Yokoyama S, Oshima T, Watanabe K... Genes Cells [details] 11918670 -
Substrate recognition of tRNA (Guanosine-2'-)-methyltransferase from Thermus thermophilus HB27. Hori H, Yamazaki N, Matsumoto T, Watanabe Y, Ueda T, Nishikawa K, Kumagai I, Watanabe K... J Biol Chem [details] 9748240 -
Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, Yokoyama S... Structure [details] 15062082 -
The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and non-substrate tRNA via an induced-fit process. Ochi A, Makabe K, Yamagami R, Hirata A, Sakaguchi R, Hou YM, Watanabe K, Nureki O, Kuwajima K, Hori H... J Biol Chem [details] 23867454 -

Links:

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