PDBsum entry 5e71

Transferase

PDB id: 5e71

Contents

Protein chain

323 a.a.

Waters ×175

PDB id:

5e71

Name:

Transferase

Title:

Crystal structure of the archaeal tRNA m2g/m22g10 methyltransferase (atrm11) from thermococcus kodakarensis

Structure:

N2, n2-dimethylguanosine tRNA methyltransferase. Chain: a. Engineered: yes

Source:

Thermococcus kodakarensis (strain atcc baa-918 / jcm 12380 / kod1). Organism_taxid: 69014. Strain: atcc baa-918 / jcm 12380 / kod1. Gene: tk0981. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.207 R-free: 0.240

Authors:

A.Hirata

Key ref:

A.Hirata et al. (2016). Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules. Nucleic Acids Res, 44, 6377-6390. PubMed id: 27325738 DOI: 10.1093/nar/gkw561

Date:

11-Oct-15 Release date: 06-Jul-16

Protein chain

Q5JID5  (Q5JID5_THEKO) -  N2, N2-dimethylguanosine tRNA methyltransferase from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

Seq: 331 a.a.

Struc: 323 a.a.

DOI no: 10.1093/nar/gkw561

Nucleic Acids Res 44:6377-6390 (2016)

PubMed id: 27325738

Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules.

A.Hirata, S.Nishiyama, T.Tamura, A.Yamauchi, H.Hori.

ABSTRACT

N(2)-methylguanosine is one of the most universal modified nucleosides required for proper function in transfer RNA (tRNA) molecules. In archaeal tRNA species, a specific S-adenosyl-L-methionine (SAM)-dependent tRNA methyltransferase (MTase), aTrm11, catalyzes formation of N(2)-methylguanosine and N(2),N(2)-dimethylguanosine at position 10. Here, we report the first X-ray crystal structures of aTrm11 from Thermococcus kodakarensis (Tko), of the apo-form, and of its complex with SAM. The structures show that TkoTrm11 consists of three domains: an N-terminal ferredoxinlike domain (NFLD), THUMP domain and Rossmann-fold MTase (RFM) domain. A linker region connects the THUMP-NFLD and RFM domains. One SAM molecule is bound in the pocket of the RFM domain, suggesting that TkoTrm11 uses a catalytic mechanism similar to that of other tRNA MTases containing an RFM domain. Furthermore, the conformation of NFLD and THUMP domains in TkoTrm11 resembles that of other tRNA-modifying enzymes specifically recognizing the tRNA acceptor stem. Our docking model of TkoTrm11-SAM in complex with tRNA, combined with biochemical analyses and pre-existing evidence, provides insights into the substrate tRNA recognition mechanism: The THUMP domain recognizes a 3'-ACCA end, and the linker region and RFM domain recognize the T-stem, acceptor stem and V-loop of tRNA, thereby causing TkoTrm11 to specifically identify its methylation site.