PDBsum entry 1uam

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Transferase PDB id
Protein chain
250 a.a. *
Waters ×103
* Residue conservation analysis
PDB id:
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)
2.20Å     R-factor:   0.220     R-free:   0.264
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
11-Mar-03     Release date:   17-Jun-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P43912  (TRMD_HAEIN) -  tRNA (guanine-N(1)-)-methyltransferase
246 a.a.
250 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - tRNA (guanine(37)-N(1))-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
+ guanine(37) in tRNA
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 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     methylation   4 terms 
  Biochemical function     tRNA (guanine(37)-N(1))-methyltransferase 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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20053984 A.Ochi, K.Makabe, K.Kuwajima, and H.Hori (2010).
Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes.
  J Biol Chem, 285, 9018-9029.  
21098051 H.Y.Chen, and Y.A.Yuan (2010).
Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase.
  J Mol Cell Biol, 2, 366-374.
PDB codes: 3ai9 3aia
20047967 J.P.Wurm, B.Meyer, U.Bahr, M.Held, O.Frolow, P.Kötter, J.W.Engels, A.Heckel, M.Karas, K.D.Entian, and J.Wöhnert (2010).
The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase.
  Nucleic Acids Res, 38, 2387-2398.  
20423905 L.M.Iyer, S.Abhiman, Souza, and L.Aravind (2010).
Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase.
  Nucleic Acids Res, 38, 5261-5279.  
20617197 M.C.Prentiss, D.J.Wales, and P.G.Wolynes (2010).
The energy landscape, folding pathways and the kinetics of a knotted protein.
  PLoS Comput Biol, 6, e1000835.  
19944101 Y.M.Hou, and J.J.Perona (2010).
Stereochemical mechanisms of tRNA methyltransferases.
  FEBS Lett, 584, 278-286.  
19077162 A.L.Mallam (2009).
How does a knotted protein fold?
  FEBS J, 276, 365-375.  
19369248 M.S.Dunstan, P.C.Hang, N.V.Zelinskaya, J.F.Honek, and G.L.Conn (2009).
Structure of the Thiostrepton Resistance Methyltransferase{middle dot}S-Adenosyl-L-methionine Complex and Its Interaction with Ribosomal RNA.
  J Biol Chem, 284, 17013-17020.
PDB code: 3gyq
19749755 S.Goto-Ito, T.Ito, M.Kuratani, Y.Bessho, and S.Yokoyama (2009).
Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation.
  Nat Struct Mol Biol, 16, 1109-1115.
PDB codes: 2zzm 2zzn
18208838 A.B.Taylor, B.Meyer, B.Z.Leal, P.Kötter, V.Schirf, B.Demeler, P.J.Hart, K.D.Entian, and J.Wöhnert (2008).
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
  Nucleic Acids Res, 36, 1542-1554.
PDB codes: 3bbd 3bbe 3bbh
19015517 A.L.Mallam, E.R.Morris, and S.E.Jackson (2008).
Exploring knotting mechanisms in protein folding.
  Proc Natl Acad Sci U S A, 105, 18740-18745.  
18538662 A.L.Mallam, S.C.Onuoha, J.G.Grossmann, and S.E.Jackson (2008).
Knotted fusion proteins reveal unexpected possibilities in protein folding.
  Mol Cell, 30, 642-648.  
18755835 E.Purta, K.H.Kaminska, J.M.Kasprzak, J.M.Bujnicki, and S.Douthwaite (2008).
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.
  RNA, 14, 2234-2244.  
18063569 N.Leulliot, M.T.Bohnsack, M.Graille, D.Tollervey, and H.Van Tilbeurgh (2008).
The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases.
  Nucleic Acids Res, 36, 629-639.
PDB codes: 2v3j 2v3k
18384044 S.Goto-Ito, T.Ito, R.Ishii, Y.Muto, Y.Bessho, and S.Yokoyama (2008).
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
  Proteins, 72, 1274-1289.
PDB code: 2yx1
18651851 T.Toyooka, T.Awai, T.Kanai, T.Imanaka, and H.Hori (2008).
Stabilization of tRNA (mG37) methyltransferase [TrmD] from Aquifex aeolicus by an intersubunit disulfide bond formation.
  Genes Cells, 13, 807-816.  
17338813 K.L.Tkaczuk, S.Dunin-Horkawicz, E.Purta, and J.M.Bujnicki (2007).
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.
  BMC Bioinformatics, 8, 73.  
17932071 S.G.Ozanick, J.M.Bujnicki, D.S.Sem, and J.T.Anderson (2007).
Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding.
  Nucleic Acids Res, 35, 6808-6819.  
17254657 S.Klimasauskas, and E.Weinhold (2007).
A new tool for biotechnology: AdoMet-dependent methyltransferases.
  Trends Biotechnol, 25, 99.  
17868690 T.Christian, and Y.M.Hou (2007).
Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases.
  J Mol Biol, 373, 623-632.  
17526524 Y.L.Lai, S.C.Yen, S.H.Yu, and J.K.Hwang (2007).
pKNOT: the protein KNOT web server.
  Nucleic Acids Res, 35, W420-W424.  
17121543 H.Takeda, T.Toyooka, Y.Ikeuchi, S.Yokobori, K.Okadome, F.Takano, T.Oshima, T.Suzuki, Y.Endo, and H.Hori (2006).
The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus.
  Genes Cells, 11, 1353-1365.  
16600901 I.Zegers, D.Gigot, F.van Vliet, C.Tricot, S.Aymerich, J.M.Bujnicki, J.Kosinski, and L.Droogmans (2006).
Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.
  Nucleic Acids Res, 34, 1925-1934.
PDB code: 2fca
16963456 K.Watanabe, O.Nureki, S.Fukai, Y.Endo, and H.Hori (2006).
Functional categorization of the conserved basic amino acid residues in TrmH (tRNA (Gm18) methyltransferase) enzymes.
  J Biol Chem, 281, 34630-34639.  
16460560 M.von Grotthuss, D.Plewczynski, K.Ginalski, L.Rychlewski, and E.I.Shakhnovich (2006).
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
  BMC Bioinformatics, 7, 53.  
16768442 T.Christian, C.Evilia, and Y.M.Hou (2006).
Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline.
  Biochemistry, 45, 7463-7473.  
  16511140 E.Pleshe, J.Truesdell, and R.T.Batey (2005).
Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 722-728.
PDB code: 1zjr
15637073 K.Watanabe, O.Nureki, S.Fukai, R.Ishii, H.Okamoto, S.Yokoyama, Y.Endo, and H.Hori (2005).
Roles of conserved amino acid sequence motifs in the SpoU (TrmH) RNA methyltransferase family.
  J Biol Chem, 280, 10368-10377.  
15987815 M.H.Renalier, N.Joseph, C.Gaspin, P.Thebault, and A.Mougin (2005).
The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP.
  RNA, 11, 1051-1063.  
16225687 P.Z.Kozbial, and A.R.Mushegian (2005).
Natural history of S-adenosylmethionine-binding proteins.
  BMC Struct Biol, 5, 19.  
15060037 K.O'Dwyer, J.M.Watts, S.Biswas, J.Ambrad, M.Barber, H.Brulé, C.Petit, D.J.Holmes, M.Zalacain, and W.M.Holmes (2004).
Characterization of Streptococcus pneumoniae TrmD, a tRNA methyltransferase essential for growth.
  J Bacteriol, 186, 2346-2354.  
18629165 T.A.White, and D.B.Kell (2004).
Comparative genomic assessment of novel broad-spectrum targets for antibacterial drugs.
  Comp Funct Genomics, 5, 304-327.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.