Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase
Synonym: aq_841
GI: 15606194
COG: COG1867
UniProt: O67010
Structures: | 3AXS | 3AXT |
Enzyme type: methyltransferase
Position of modification - modification: t:26 - m2,2G
t:27 - m2,2G


PDB Structures:


3AXS

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Archaeal and eukaryotic tRNA (N(2),N(2)-guanine)-dimethyltransferase (Trm1) produces N(2),N(2)-dimethylguanine at position 26 in tRNA. In contrast, Trm1 from Aquifex aeolicus, a hyper-thermophilic eubacterium, modifies G27 as well as G26. Here, a gel mobility shift assay revealed that the T-arm in tRNA is the binding site of A. aeolicus Trm1. To address the multisite specificity, we performed an x-ray crystal structure study. The overall structure of A. aeolicus Trm1 is similar to that of archaeal Trm1, although there is a zinc-cysteine cluster in the C-terminal domain of A. aeolicus Trm1. The N-terminal domain is a typical catalytic domain of S-adenosyl-l-methionine-dependent methyltransferases. On the basis of the crystal structure and amino acid sequence alignment, we prepared 30 mutant Trm1 proteins. These mutant proteins clarified residues important for S-adenosyl-l-methionine binding and enabled us to propose a hypothetical reaction mechanism. Furthermore, the tRNA-binding site was also elucidated by methyl transfer assay and gel mobility shift assay. The electrostatic potential surface models of A. aeolicus and archaeal Trm1 proteins demonstrated that the distribution of positive charges differs between the two proteins. We constructed a tRNA-docking model, in which the T-arm structure was placed onto the large area of positive charge, which is the expected tRNA-binding site, of A. aeolicus Trm1. In this model, the target G26 base can be placed near the catalytic pocket; however, the nucleotide at position 27 gains closer access to the pocket. Thus, this docking model introduces a rational explanation of the multisite specificity of A. aeolicus Trm1.

Download RCSB-PDB Structures:

Pdb Files   3AXS.pdb   3AXT.pdb  
Pdbx/mmCIF Files   3AXS.cif   3AXT.cif  


Protein sequence:

MEIVQEGIAKIIVPEIPKTVSSDMPVFYNPRMRVNRDLAVLGLEYLCKKLGRPVKVADPLSASGIRAIRFLLETSCVEKAYANDISSKAIEIMKENFKLNNIPEDRYEIHGMEANFFLRKEWGFGFDYVDLDPFGTPVPFIESVALSMKRGGILSLTATDTAPLSGTYPKTCMRRYMARPLRNEFKHEVGIRILIKKVIELAAQYDIAMIPIFAYSHLHYFKLFFVKERGVEKVDKLIEQFGYIQYCFNCMNREVVTDLYKFKEKCPHCGSKFHIGGPLWIGKLWDEEFTNFLYEEAQKREEIEKETKRILKLIKEESQLQTVGFYVLSKLAEKVKLPAQPPIRIAVKFFNGVRTHFVGDGFRTNLSFEEVMKKMEELKEKQKEFLEKKKQG

Comments:

Activity tested in vitro and detected in cell extract.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m2G RNA tRNA 26 ACG ACG tRNAArgACG D-loop Prokaryotic Cytosol
G:m2G RNA tRNA 26 ACG ACG tRNAArgACG D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 26 GUC GUC tRNAAspGUC D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 26 GCC GCC tRNAGlyGCC D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 26 GUG GUG tRNAHysGUG D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 26 CGG CGG tRNAProCGG D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 26 CAU CAU tRNAMetfCAU D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 26 GCA GCA tRNACysGCA D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 26 CAG CAG tRNALeuCAG D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 26 UUC UUC tRNAGluUUC D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 26 GUA GUA tRNATyrGUA D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 26 UUG UUG tRNAGlnUUG D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 ACG ACG tRNAArgACG D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 GUC GUC tRNAAspGUC D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 GCC GCC tRNAGlyGCC D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 GUG GUG tRNAHysGUG D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 CGG CGG tRNAProCGG D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 CAU CAU tRNAMetfCAU D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 GCA GCA tRNACysGCA D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 CAG CAG tRNALeuCAG D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 UUC UUC tRNAGluUUC D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 GUA GUA tRNATyrGUA D-loop Prokaryotic Cytosol 19491098   
G:m2G RNA tRNA 27 UUG UUG tRNAGlnUUG D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 ACG ACG tRNAArgACG D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 GUC GUC tRNAAspGUC D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 GCC GCC tRNAGlyGCC D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 GUG GUG tRNAHysGUG D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 CGG CGG tRNAProCGG D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 CAU CAU tRNAMetfCAU D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 GCA GCA tRNACysGCA D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 CAG CAG tRNALeuCAG D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 UUC UUC tRNAGluUUC D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 GUA GUA tRNATyrGUA D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 26 UUG UUG tRNAGlnUUG D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 ACG ACG tRNAArgACG D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 GUC GUC tRNAAspGUC D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 GCC GCC tRNAGlyGCC D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 GUG GUG tRNAHysGUG D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 CGG CGG tRNAProCGG D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 CAU CAU tRNAMetfCAU D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 GCA GCA tRNACysGCA D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 CAG CAG tRNALeuCAG D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 UUC UUC tRNAGluUUC D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 GUA GUA tRNATyrGUA D-loop Prokaryotic Cytosol 19491098   
m2G:m2,2G RNA tRNA 27 UUG UUG tRNAGlnUUG D-loop Prokaryotic Cytosol 19491098   



Publications:

Title Authors Journal Details PubMed Id DOI
Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure. Awai T, Ochi A, Ihsanawati, Sengoku T, Hirata A, Bessho Y, Yokoyama S, Hori H J Biol Chem [details] 21844194 -
Aquifex aeolicus tRNA (N2,N2-guanine)-dimethyltransferase (Trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in tRNA. Awai T, Kimura S, Tomikawa C, Ochi A, Ihsanawati, Bessho Y, Yokoyama S, Ohno S, Nishikawa K, Yokogawa T, Suzuki T, Hori H J Biol Chem [details] 19491098 -
Identification of Aquifex aeolicus tRNA (m2(2G26) methyltransferase gene. Takeda H, Hori H, Endo Y Nucleic Acids Res Suppl. [details] 12903189 -
Aquifex aeolicus Trm1[tRNA (m2(2)G26) methyltransferase] has a novel recognition mechanism of the substrate RNA. Awai T, Takehara T, Takeda H, Hori H Nucleic Acids Symp Ser (Oxf) [details] 17150754 -