PDBsum entry 4jal

Transferase

PDB id: 4jal

Contents

Protein chains

156 a.a.

Ligands

SAH ×2

EPE

EDO ×2

Waters ×48

PDB id:

4jal

Name:

Transferase

Title:

Crystal structure of tRNA (um34/cm34) methyltransferase trml from escherichia coli with sah

Structure:

tRNA (cytidine(34)-2'-o)-methyltransferase. Chain: a, b. Synonym: tRNA (cytidine/uridine-2'-o-)-methyltransferase trml. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: trml, yibk, b3606, jw3581. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.214 R-free: 0.245

Authors:

R.J.Liu,M.Zhou,E.D.Wang

Key ref:

R.J.Liu et al. (2013). The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL. Nucleic Acids Res, 41, 7828-7842. PubMed id: 23804755 DOI: 10.1093/nar/gkt568

Date:

18-Feb-13 Release date: 31-Jul-13

Protein chains

P0AGJ7  (TRML_ECOLI) -  tRNA (cytidine(34)-2'-O)-methyltransferase from Escherichia coli (strain K12)

Seq: 157 a.a.

Struc: 156 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.1.1.207 - tRNA (cytidine(34)-2'-O)-methyltransferase.
• Reaction:
  1. cytidine₃₄ in tRNA + S-adenosyl-L-methionine = 2'-O- methylcytidine₃₄ in tRNA + S-adenosyl-L-homocysteine + H⁺
  2. 5-carboxymethylaminomethyluridine₃₄ in tRNA(Leu) + S-adenosyl-L- methionine = 5-carboxymethylaminomethyl-2'-O-methyluridine₃₄ in tRNA(Leu) + S-adenosyl-L-homocysteine + H⁺

cytidine(34) in tRNA + S-adenosyl-L-methionine = 2'-O- methylcytidine(34) in tRNA + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

5-carboxymethylaminomethyluridine(34) in tRNA(Leu) + S-adenosyl-L- methionine = 5-carboxymethylaminomethyl-2'-O-methyluridine(34) in tRNA(Leu) + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

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

reference

DOI no: 10.1093/nar/gkt568

Nucleic Acids Res 41:7828-7842 (2013)

PubMed id: 23804755

The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL.

R.J.Liu, M.Zhou, Z.P.Fang, M.Wang, X.L.Zhou, E.D.Wang.

ABSTRACT

Unlike other transfer RNAs (tRNA)-modifying enzymes from the SPOUT methyltransferase superfamily, the tRNA (Um34/Cm34) methyltransferase TrmL lacks the usual extension domain for tRNA binding and consists only of a SPOUT domain. Both the catalytic and tRNA recognition mechanisms of this enzyme remain elusive. By using tRNAs purified from an Escherichia coli strain with the TrmL gene deleted, we found that TrmL can independently catalyze the methyl transfer from S-adenosyl-L-methionine to and isoacceptors without the involvement of other tRNA-binding proteins. We have solved the crystal structures of TrmL in apo form and in complex with S-adenosyl-homocysteine and identified the cofactor binding site and a possible active site. Methyltransferase activity and tRNA-binding affinity of TrmL mutants were measured to identify residues important for tRNA binding of TrmL. Our results suggest that TrmL functions as a homodimer by using the conserved C-terminal half of the SPOUT domain for catalysis, whereas residues from the less-conserved N-terminal half of the other subunit participate in tRNA recognition.