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PDBsum entry 1v2x
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Transferase PDB id
1v2x

 

 

 

 

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Contents
Protein chain
191 a.a. *
Ligands
PO4 ×2
SAM
Waters ×190
* Residue conservation analysis
PDB id:
1v2x
Name: Transferase
Title: Trmh
Structure: tRNA (gm18) methyltransferase. Chain: a. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
Biol. unit: Dimer (from PQS)
Resolution:
1.50Å     R-factor:   0.225     R-free:   0.277
Authors: O.Nureki,K.Watanabe,S.Fukai,R.Ishii,Y.Endo,H.Hori,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
O.Nureki et al. (2004). Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure, 12, 593-602. PubMed id: 15062082 DOI: 10.1016/j.str.2004.03.003
Date:
17-Oct-03     Release date:   04-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SM16  (TRMH_THET8) -  tRNA (guanosine(18)-2'-O)-methyltransferase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		194 a.a.
191 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.34  - tRNA (guanosine(18)-2'-O)-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: guanosine18 in tRNA + S-adenosyl-L-methionine = 2'-O- methylguanosine18 in tRNA + S-adenosyl-L-homocysteine + H+
guanosine(18) in tRNA
 +
S-adenosyl-L-methionine
Bound ligand (Het Group name = SAM)
corresponds exactly 		= 2'-O- methylguanosine(18) in tRNA
 + S-adenosyl-L-homocysteine
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/j.str.2004.03.003 Structure 12:593-602 (2004)
PubMed id: 15062082  
 
 
Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme.
O.Nureki, K.Watanabe, S.Fukai, R.Ishii, Y.Endo, H.Hori, S.Yokoyama.
 
  ABSTRACT  
 
The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 A resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2'-OH group for methylation.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Docking Model of the tRNA D-Arm and the TrmH Dimer
Each subunit of the TrmH dimer is colored pink or cyan, with the knotted polypeptide magenta or blue, respectively. The tRNA D-arm is shown in green, with the recognized G15, G18, and G19 indicated. The helical subdomain of one monomer recognizing the tRNA D-stem is colored in yellow. The whole tRNA structure, transparently shown in green, has serious clashes with the catalytic domain of one monomer. 		Figure 4.
Figure 4. The RNA-Dependent Catalytic Mechanism
The simulated omit F[o] − F[c] maps for the tightly bound sulfate ion and the water molecule, contoured at 4.0 σ, are shown. The bound AdoMet cofactor is shown in green. Based on the sulfate ion (phosphate group analog) and the water molecule, Gua18 is modeled onto the active site pocket. Arg41 from the other subunit of the dimer, indicated in purple, might act as a catalytic base that withdraws a proton from the 2′-OH group of Gua18 and allows it to attack the methyl group of AdoMet. Possible hydrogen bonds are indicated with dotted lines.
 
  The above figures are reprinted by permission from Cell Press: Structure (2004, 12, 593-602) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19934251 C.Tomikawa, T.Yokogawa, T.Kanai, and H.Hori (2010).
N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network.
  Nucleic Acids Res, 38, 942-957.  
20134421 K.Takai, T.Sawasaki, and Y.Endo (2010).
Practical cell-free protein synthesis system using purified wheat embryos.
  Nat Protoc, 5, 227-238.  
19077162 A.L.Mallam (2009).
How does a knotted protein fold?
  FEBS J, 276, 365-375.  
  20582239 T.Petrossian, and S.Clarke (2009).
Bioinformatic Identification of Novel Methyltransferases.
  Epigenomics, 1, 163-175.  
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.  
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
18755836 R.Ero, L.Peil, A.Liiv, and J.Remme (2008).
Identification of pseudouridine methyltransferase in Escherichia coli.
  RNA, 14, 2223-2233.  
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.  
18158303 Y.Araiso, S.Palioura, R.Ishitani, R.L.Sherrer, P.O'Donoghue, J.Yuan, H.Oshikane, N.Domae, J.Defranco, D.Söll, and O.Nureki (2008).
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation.
  Nucleic Acids Res, 36, 1187-1199.
PDB code: 2z67
18509492 Z.Nie, R.Zhou, J.Chen, D.Wang, Z.Lv, P.He, X.Wang, H.Shen, X.Wu, and Y.Zhang (2008).
Subcellular localization and RNA interference of an RNA methyltransferase gene from silkworm, Bombyx mori.
  Comp Funct Genomics, (), 571023.  
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.  
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.  
17374386 X.Cheng, and X.Zhang (2007).
Structural dynamics of protein lysine methylation and demethylation.
  Mutat Res, 618, 102-115.  
16848900 E.Purta, F.van Vliet, K.L.Tkaczuk, S.Dunin-Horkawicz, H.Mori, L.Droogmans, and J.M.Bujnicki (2006).
The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase.
  BMC Mol Biol, 7, 23.  
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
16395670 J.Y.Tsai, B.T.Chen, H.C.Cheng, H.Y.Chen, N.W.Hsaio, P.C.Lyu, and Y.J.Sun (2006).
Crystal structure of HP0242, a hypothetical protein from Helicobacter pylori with a novel fold.
  Proteins, 62, 1138-1143.
PDB code: 2bo3
16433904 K.L.Tkaczuk, A.Obarska, and J.M.Bujnicki (2006).
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.
  BMC Evol Biol, 6, 6.  
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.  
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.  
16537549 Z.Liu, E.L.Zechiedrich, and H.S.Chan (2006).
Inferring global topology from local juxtaposition geometry: interlinking polymer rings and ramifications for topoisomerase action.
  Biophys J, 90, 2344-2355.  
  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.  
15869391 X.Cheng, R.E.Collins, and X.Zhang (2005).
Structural and sequence motifs of protein (histone) methylation enzymes.
  Annu Rev Biophys Biomol Struct, 34, 267-294.  
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.

 

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