PDBsum entry 5hjj

Transferase

PDB id: 5hjj

Contents

Protein chain

348 a.a.

Waters ×332

PDB id:

5hjj

Name:

Transferase

Title:

Crystal structure of pyrococcus abyssi trm5a

Structure:

tRNA (guanine(37)-n1)-methyltransferase trm5a. Chain: a. Synonym: m1g-methyltransferase,tRNA [gm37] methyltransferase. Engineered: yes

Source:

Pyrococcus abyssi (strain ge5 / orsay). Organism_taxid: 272844. Strain: ge5 / orsay. Gene: trm5a, pyrab01130, pab2272. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.199 R-free: 0.245

Authors:

W.Xie,C.Wang,Q.Jia

Key ref:

C.Wang et al. (2016). Crystal structures of the bifunctional tRNA methyltransferase Trm5a. Sci Rep, 6, 33553. PubMed id: 27629654 DOI: 10.1038/srep33553

Date:

13-Jan-16 Release date: 12-Oct-16

Protein chain

Q9V2G1  (TAW22_PYRAB) -  tRNA (guanine(37)-N(1))/4-demethylwyosine(37)-methyltransferase Taw22 from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 333 a.a.

Struc: 348 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.1.1.- - ?????
• Enzyme class 2: E.C.2.1.1.228 - tRNA (guanine(37)-N(1))-methyltransferase.
• Reaction: guanosine₃₇ in tRNA + S-adenosyl-L-methionine = N₁- methylguanosine₃₇ in tRNA + S-adenosyl-L-homocysteine + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/srep33553

Sci Rep 6:33553 (2016)

PubMed id: 27629654

Crystal structures of the bifunctional tRNA methyltransferase Trm5a.

C.Wang, Q.Jia, R.Chen, Y.Wei, J.Li, J.Ma, W.Xie.

ABSTRACT

tRNA methyltransferase Trm5 catalyses the transfer of a methyl group from S-adenosyl-L-methionine to G37 in eukaryotes and archaea. The N1-methylated guanosine is the product of the initial step of the wyosine hypermodification, which is essential for the maintenance of the reading frame during translation. As a unique member of this enzyme family, Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4-demethylwyosine at position 37 to produce isowyosine, but the mechanism for the double methylation is poorly understood. Here we report four crystal structures of PaTrm5a ranging from 1.7- to 2.3-Å, in the apo form or in complex with various SAM analogues. These structures reveal that Asp243 specifically recognises the base moiety of SAM at the active site. Interestingly, the protein in our structures all displays an extended conformation, quite different from the well-folded conformation of Trm5b from Methanocaldococcus jannaschii reported previously, despite their similar overall architectures. To rule out the possibilities of crystallisation artefacts, we conducted the fluorescence resonance energy transfer (FRET) experiments. The FRET data suggested that PaTrm5a adopts a naturally extended conformation in solution, and therefore the open conformation is a genuine state of PaTrm5a.