PDBsum entry: 1ual

Transferase

PDB id: 1ual

Contents

Protein chain

243 a.a. *

Ligands

SAH

Waters ×278

* Residue conservation analysis

PDB id:

1ual

Name:

Transferase

Title:

Crystal structure of tRNA(m1g37)methyltransferase: insight i recognition

Structure:

tRNA (guanine-n(1)-)-methyltransferase. Chain: a. Synonym: tRNA(m1g37)methyltransferase. Engineered: yes

Source:

Haemophilus influenzae. Organism_taxid: 727. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.80Å R-factor: 0.184 R-free: 0.215

Authors:

H.J.Ahn,H.-W.Kim,H.-J.Yoon,B.I.Lee,S.W.Suh,J.K.Yang

Key ref:

H.J.Ahn et al. (2003). Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition. EMBO J, 22, 2593-2603. PubMed id: 12773376 DOI: 10.1093/emboj/cdg269

Date:

11-Mar-03 Release date: 17-Jun-03

Protein chain

P43912  (TRMD_HAEIN) -  tRNA (guanine-N(1)-)-methyltransferase

Seq: 246 a.a.

Struc: 243 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.228 - tRNA (guanine(37)-N(1))-methyltransferase.
• Reaction: S-adenosyl-L-methionine + guanine₃₇ in tRNA = S-adenosyl-L-homocysteine + N₁-methylguanine₃₇ in tRNA

S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine (Bound ligand (Het Group name = SAH) corresponds exactly) + N(1)-methylguanine(37) in tRNA

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: methylation (2 terms)
• Biochemical function: transferase activity (4 terms)

Added reference

DOI no: 10.1093/emboj/cdg269

EMBO J 22:2593-2603 (2003)

PubMed id: 12773376

Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition.

H.J.Ahn, H.W.Kim, H.J.Yoon, B.I.Lee, S.W.Suh, J.K.Yang.

ABSTRACT

tRNA(m(1)G37)methyltransferase (TrmD) catalyzes the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to G(37) within a subset of bacterial tRNA species, which have a G residue at the 36th position. The modified guanosine is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation. Here we report four crystal structures of TrmD from Haemophilus influenzae, as binary complexes with either AdoMet or S-adenosyl-L-homocysteine (AdoHcy), as a ternary complex with AdoHcy and phosphate, and as an apo form. This first structure of TrmD indicates that it functions as a dimer. It also suggests the binding mode of G(36)G(37) in the active site of TrmD and the catalytic mechanism. The N-terminal domain has a trefoil knot, in which AdoMet or AdoHcy is bound in a novel, bent conformation. The C-terminal domain shows structural similarity to trp repressor. We propose a plausible model for the TrmD(2)-tRNA(2) complex, which provides insights into recognition of the general tRNA structure by TrmD.

Selected figure(s)

Figure 2.
Figure 2 'SPOUT class MTase fold' versus 'consensus MTase fold'. (A–D) Figures in (A) are for TrmD from H.influenzae, (B) for RmlB from E.coli (PDB entry 1GZ0), (C) for RrmA from T.thermophilus (PDB entry 1IPA), and (D) for MT0001 from M.thermoautotrophicum (PDB entry 1K3R). Figures in the first row are topology diagrams for the 'SPOUT domain' of each protein. Common -helices and -strands are denoted by circles or triangles filled with gray color. Figures in the second row show the dimer interface between the two 'SPOUT domains', each of which comes from different subunits. One monomer is colored in light scarlet and the other in light blue. The two -helices ( I' and VI') and part of the loop VI/aVI' are highlighted in deep colors, and the two -helices are indicated by Roman numbers, whose definitions are as in (E). (E) Topology diagram of the 'SPOUT class MTase fold', as defined in this study. The secondary structure elements that are common to the four SPOUT class MTases are shaded. (F) Topology diagram of the previously defined 'consensus MTase fold'.

Figure 4.
Figure 4 AdoMet/AdoHcy binding mode. (A–C) Stereo diagrams of AdoMet in the binary complex and AdoHcy in binary and ternary complexes, respectively. AdoMet/AdoHcy is shown in stick models and colored using the same scheme as in Figure 1A. The residues interacting with AdoMet/AdoHcy are also shown in stick models and their carbon atoms are colored in gray. Water molecules are shown as red balls. Dotted lines represent possible hydrogen bonds between AdoMet/AdoHcy and TrmD or water molecules. The loops colored in yellow are from one protomer and that in purple is from the other protomer. An asterisk after the residue number denotes that the residue comes from the other protomer. In (C), G113 (labeled in red) supports the twist conformation of the ribose ring of AdoHcy through a hydrogen bond, indicated by a red, dotted line. (D) [A]-weighted simulated annealing omit map for the binary complex around AdoHcy, contoured at 1.0 . (E) A novel, bent conformation of AdoMet bound in TrmD (thick lines in green). AdoMet and AdoHcy observed in various MTases are superimposed in the ribose ring. A thin stick model colored in blue represents another distinct bent conformation of AdoHcy in CbiF (PDB entry 1CBF). Extended conformations that are observed most frequently are drawn in thin stick models: AdoMet bound in VP39 (1VPT), ErmC' (1QAO), FtsJ (1EIZ), M.TaqI (2ADM), M.HhaI (1HMY), PIMT (1JG4) and COMT (1VID) are colored in brown, yellow, red, cyan, black, pink and gray, respectively. AdoHcy bound in CheR (1AF7) is in violet. (F) Superposition of AdoMet and AdoHcy observed in three TrmD complex structures. They are superimposed in the adenine part. Oxygen atoms are colored in red, nitrogen in blue and sulfur in yellow. Carbon atoms in AdoMet are colored in green, those in AdoHcy of the binary complex in light pink, and those in AdoHcy of the ternary complex in gray.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 2593-2603) copyright 2003.

Figures were selected by an automated process.