PDBsum entry 1ipa

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protein links
Transferase PDB id
Protein chain
258 a.a. *
Waters ×151
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of RNA 2'-o ribose methyltransferase
Structure: RNA 2'-o-ribose methyltransferase. Chain: a. Synonym: rrmh. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.40Å     R-factor:   0.226     R-free:   0.286
Authors: O.Nureki,M.Shirouzu,K.Hashimoto,R.Ishitani,T.Terada, M.Tamakoshi,T.Oshima,M.Chijimatsu,K.Takio,D.G.Vassylyev, T.Shibata,Y.Inoue,S.Kuramitsu,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
O.Nureki et al. (2002). An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallogr D Biol Crystallogr, 58, 1129-1137. PubMed id: 12077432 DOI: 10.1107/S0907444902006601
02-May-01     Release date:   10-Jul-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q7SID4  (Q7SID4_THETH) -  Transferase
274 a.a.
258 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     methylation   3 terms 
  Biochemical function     transferase activity     4 terms  


DOI no: 10.1107/S0907444902006601 Acta Crystallogr D Biol Crystallogr 58:1129-1137 (2002)
PubMed id: 12077432  
An enzyme with a deep trefoil knot for the active-site architecture.
O.Nureki, M.Shirouzu, K.Hashimoto, R.Ishitani, T.Terada, M.Tamakoshi, T.Oshima, M.Chijimatsu, K.Takio, D.G.Vassylyev, T.Shibata, Y.Inoue, S.Kuramitsu, S.Yokoyama.
Knots in polypeptide chains have been found in very few proteins. Only two proteins are considered to have a shallow 'trefoil' knot, which tucks a few residues at one end of the chain through a loop exposed on the protein surface. Recently, another protein was found by a mathematical algorithm to have a deep 'figure-of-eight' knot which had not been visually identified. In the present study, the crystal structure of a hypothetical RNA 2'-O-ribose methyltransferase from Thermus thermophilus (RrmA) was determined at 2.4 A resolution and a deep trefoil knot was found for the first time. The present knot is formed by the threading of a 44-residue polypeptide chain through a 41-residue loop and is better defined than the previously reported knots. Two of the three catalytic residues conserved in the 2'-O-ribose methyltransferase family are located in the knotting loop and in the knotted carboxy-terminal chain, which is the first observation that the enzyme active site is constructed right on the knot. On the other hand, the amino-terminal domain exhibits a geometrical similarity to the ribosomal proteins which recognize an internal loop of RNA.
  Selected figure(s)  
Figure 5.
Figure 5 (a)-(c) Protein knots (stereoviews) and their topologies. The `knotting loop' and the `knotted chain' are coloured blue and red, respectively. The `knotting point' is indicated with a magenta rectangle. (a) The shallow trefoil knot of MAT (Takusagawa & Kamitori, 1996[Takusagawa, F. & Kamitori, K. (1996). J. Am. Chem. Soc. 118, 8945-8946.]). (b) The deep trefoil knot of RrmA (this work). (c) The deep figure-of-eight knot of AIR (Taylor, 2000[Taylor, W. R. (2000). Nature (London), 406, 916-919.]). (d) Interactions between the threaded polypeptide chain and the `knotting loop'. Hydrogen-bonding interactions are shown by dotted magenta lines. The amino-acid residues that form a hydrophobic core are indicated.
Figure 6.
Figure 6 (a) Concentration distribution of RrmA (0.34 mg ml-1) during the sedimentation-equilibrium experiment at 15 000 rev min-1. (b) The structure of the RrmA dimer. The `knotted carboxy-terminal chain' and the remainder of one subunit are coloured red and orange, respectively, and the corresponding chains of the other subunit are coloured green and cyan, respectively. The amino-acid residues involved in the molecular dimerization are indicated as ball-and-stick models. The twofold axis is denoted by a red ellipse.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1129-1137) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21108865 B.Liang, and H.Li (2011).
Structures of ribonucleoprotein particle modification enzymes.
  Q Rev Biophys, 44, 95.  
  20944210 A.Andreeva, and A.G.Murzin (2010).
Structural classification of proteins and structural genomics: new insights into protein folding and evolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1190-1197.  
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
19077162 A.L.Mallam (2009).
How does a knotted protein fold?
  FEBS J, 276, 365-375.  
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.  
19064918 J.I.SuĊ‚kowska, P.Sulkowski, P.Szymczak, and M.Cieplak (2008).
Stabilizing effect of knots on proteins.
  Proc Natl Acad Sci U S A, 105, 19714-19719.  
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.  
17395198 D.R.Boutz, D.Cascio, J.Whitelegge, L.J.Perry, and T.O.Yeates (2007).
Discovery of a thermophilic protein complex stabilized by topologically interlinked chains.
  J Mol Biol, 368, 1332-1344.
PDB code: 2ibp
17567748 J.W.Blankenship, and P.E.Dawson (2007).
Threading a peptide through a peptide: protein loops, rotaxanes, and knots.
  Protein Sci, 16, 1249-1256.  
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.  
17368671 S.Wallin, K.B.Zeldovich, and E.I.Shakhnovich (2007).
The folding mechanics of a knotted protein.
  J Mol Biol, 368, 884-893.  
17967433 T.O.Yeates, T.S.Norcross, and N.P.King (2007).
Knotted and topologically complex proteins as models for studying folding and stability.
  Curr Opin Chem Biol, 11, 595-603.  
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.  
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
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.  
16669784 N.C.Rockwell, Y.S.Su, and J.C.Lagarias (2006).
Phytochrome structure and signaling mechanisms.
  Annu Rev Plant Biol, 57, 837-858.  
  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
16292304 J.R.Wagner, J.S.Brunzelle, K.T.Forest, and R.D.Vierstra (2005).
A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome.
  Nature, 438, 325-331.
PDB code: 1ztu
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.  
15036155 A.F.Yakunin, A.A.Yee, A.Savchenko, A.M.Edwards, and C.H.Arrowsmith (2004).
Structural proteomics: a tool for genome annotation.
  Curr Opin Chem Biol, 8, 42-48.  
15152095 B.S.Nield, R.D.Willows, A.E.Torda, M.R.Gillings, A.J.Holmes, K.M.Nevalainen, H.W.Stokes, and B.C.Mabbutt (2004).
New enzymes from environmental cassette arrays: functional attributes of a phosphotransferase and an RNA-methyltransferase.
  Protein Sci, 13, 1651-1659.  
  15215454 K.Ginalski, M.von Grotthuss, N.V.Grishin, and L.Rychlewski (2004).
Detecting distant homology with Meta-BASIC.
  Nucleic Acids Res, 32, W576-W581.  
15296518 R.I.Sadreyev, and N.V.Grishin (2004).
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments.
  BMC Bioinformatics, 5, 106.  
15215527 Y.Ye, and A.Godzik (2004).
Database searching by flexible protein structure alignment.
  Protein Sci, 13, 1841-1850.  
14579367 A.Seto, M.Shirouzu, T.Terada, K.Murayama, S.Kuramitsu, and S.Yokoyama (2003).
Crystal structure of a hypothetical protein, TT1725, from Thermus thermophilus HB8 at 1.7 A resolution.
  Proteins, 53, 768-771.
PDB code: 1j27
14517985 F.Forouhar, J.Shen, R.Xiao, T.B.Acton, G.T.Montelione, and L.Tong (2003).
Functional assignment based on structural analysis: crystal structure of the yggJ protein (HI0303) of Haemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot.
  Proteins, 53, 329-332.
PDB code: 1nxz
12773376 H.J.Ahn, H.W.Kim, H.J.Yoon, B.I.Lee, S.W.Suh, and J.K.Yang (2003).
Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition.
  EMBO J, 22, 2593-2603.
PDB codes: 1uaj 1uak 1ual 1uam
12826405 H.L.Schubert, R.M.Blumenthal, and X.Cheng (2003).
Many paths to methyltransfer: a chronicle of convergence.
  Trends Biochem Sci, 28, 329-335.  
12707282 K.Yokoyama, M.Nakano, H.Imamura, M.Yoshida, and M.Tamakoshi (2003).
Rotation of the proteolipid ring in the V-ATPase.
  J Biol Chem, 278, 24255-24258.  
12689347 M.A.Kurowski, J.M.Sasin, M.Feder, J.Debski, and J.M.Bujnicki (2003).
Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.
  BMC Bioinformatics, 4, 9.  
12486711 T.I.Zarembinski, Y.Kim, K.Peterson, D.Christendat, A.Dharamsi, C.H.Arrowsmith, A.M.Edwards, and A.Joachimiak (2003).
Deep trefoil knot implicated in RNA binding found in an archaebacterial protein.
  Proteins, 50, 177-183.
PDB code: 1k3r
12389038 S.A.Jacobs, J.M.Harp, S.Devarakonda, Y.Kim, F.Rastinejad, and S.Khorasanizadeh (2002).
The active site of the SET domain is constructed on a knot.
  Nat Struct Biol, 9, 833-838.
PDB codes: 1mt6 1muf
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.