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:	Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme
Classification:	TRANSFERASE
Technique:	X-Ray Diffraction
Resolution:	1.5
R value free:	0.277
R value observed:	0.225
R value work:	0.225

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.

Search:

Reaction	Substrate	SubstrateType	Position	(Anti)Codon	Modified (Anti)Codon	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	tRNA^Ala_CGC-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GGC-1	GGC-1	tRNA^Ala_GGC-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TGC-1	TGC-1	tRNA^Ala_TGC-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	ACG-1	ACG-1	tRNA^Arg_ACG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CCG-1	CCG-1	tRNA^Arg_CCG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CCT-1	CCT-1	tRNA^Arg_CCT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TCT-1	TCT-1	tRNA^Arg_TCT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GTT-1	GTT-1	tRNA^Asn_GTT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GTC-1	GTC-1	tRNA^Asp_GTC-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GCA-1	GCA-1	tRNA^Cys_GCA-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CTG-1	CTG-1	tRNA^Gln_CTG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TTG-1	TTG-1	tRNA^Gln_TTG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CTC-1	CTC-1	tRNA^Glu_CTC-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CTC-2	CTC-2	tRNA^Glu_CTC-2	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TTC-1	TTC-1	tRNA^Glu_TTC-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CCC-1	CCC-1	tRNA^Gly_CCC-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GCC-1	GCC-1	tRNA^Gly_GCC-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GTG-1	GTG-1	tRNA^His_GTG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GAT-1	GAT-1	tRNA^Ile_GAT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CAT-1	CAT-1	tRNA^Ile2_CAT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CAA-1	CAA-1	tRNA^Leu_CAA-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CAG-1	CAG-1	tRNA^Leu_CAG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GAG-1	GAG-1	tRNA^Leu_GAG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TAA-1	TAA-1	tRNA^Leu_TAA-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TAG-1	TAG-1	tRNA^Leu_TAG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CTT-1	CTT-1	tRNA^Lys_CTT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TTT-1	TTT-1	tRNA^Lys_TTT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CAT-1	CAT-1	tRNA^Met_CAT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CAT-2	CAT-2	tRNA^Met_CAT-2	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GAA-1	GAA-1	tRNA^Phe_GAA-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CGG-1	CGG-1	tRNA^Pro_CGG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GGG-1	GGG-1	tRNA^Pro_GGG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TGG-1	TGG-1	tRNA^Pro_TGG-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CGA-1	CGA-1	tRNA^Ser_CGA-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GCT-1	GCT-1	tRNA^Ser_GCT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GGA-1	GGA-1	tRNA^Ser_GGA-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TGA-1	TGA-1	tRNA^Ser_TGA-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CGT-1	CGT-1	tRNA^Thr_CGT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GGT-1	GGT-1	tRNA^Thr_GGT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TGT-1	TGT-1	tRNA^Thr_TGT-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CCA-1	CCA-1	tRNA^Trp_CCA-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GTA-1	GTA-1	tRNA^Tyr_GTA-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	CAC-1	CAC-1	tRNA^Val_CAC-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	GAC-1	GAC-1	tRNA^Val_GAC-1	D-stem loop	Prokaryotic Cytosol	23867454
G:Gm	RNA	tRNA	18	TAC-1	TAC-1	tRNA^Val_TAC-1	D-stem loop	Prokaryotic Cytosol	23867454


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Showing 1 to 46 of 46 entries

Publications:

Search:

Title	Authors	Journal	Details	PubMed Id	DOI
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	-
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	-
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	-


Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme.
Identification and characterization of tRNA (Gm18) methyltransferase from Thermus thermophilus HB8: domain structure and conserved amino acid sequence motifs.
Substrate recognition of tRNA (Guanosine-2'-)-methyltransferase from Thermus thermophilus HB27.
The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and non-substrate tRNA via an induced-fit process.

Showing 1 to 4 of 4 entries

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