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.







Publications:

Links:

_PubMed_