5GRA

Crystal structure of TrmJ from Z. mobilis ZM4

Summary for 5GRA

• Entry DOI: 10.2210/pdb5gra/pdb
• Descriptor: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ (2 entities in total)
• Functional Keywords: methyltransferase, trna, trmj, transferase
• Biological source: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
• Cellular location: Cytoplasm : Q5NN83
• Total number of polymer chains: 2
• Total formula weight: 52932.99

Authors

Gu, D.-H.,Kim, J.-S. (deposition date: 2016-08-09, release date: 2017-06-21, Last modification date: 2024-03-20)

Primary citation

Gu, D.-H.,Park, M.-Y.,Kim, J.-S.
An asymmetric dimeric structure of TrmJ tRNA methyltransferase from Zymomonas mobilis with a flexible C-terminal dimer
Biochem. Biophys. Res. Commun., 488:407-412, 2017

PubMed Abstract: The tRNA methyltransferase J (TrmJ) and D (TrmD) catalyze the transferring reaction of a methyl group to the tRNA anticodon loop. They commonly have the N-terminal domain (NTD) and the C-terminal domain (CTD). Whereas two monomeric CTDs symmetrically interact with a dimeric NTD in TrmD, a CTD dimer has exhibited an asymmetric interaction with the NTD dimer in the presence of a product. The elucidated apo-structure of the full-length TrmJ from Zymomonas mobilis ZM4 shows a dimeric CTD that asymmetrically interacts with the NTD dimer, thereby distributing non-symmetrical potential charge on the both side of the protein surface. Comparison with the product-bound structures reveals a local re-orientation of the two arginine-containing loop at the active site, which interacts with the product. Further, the CTD dimers have diverse orientations compared to the NTD dimers, suggesting their flexibility. These data indicate that an asymmetric interaction between the NTD dimer and the CTD dimer is a common structural feature among TrmJ proteins, regardless of the presence of a substrate or a product.

PubMed: 28506829
DOI: 10.1016/j.bbrc.2017.05.068

Experimental method

X-RAY DIFFRACTION (3.005 Å)