PDBsum entry 1gz0

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protein Protein-protein interface(s) links
Transferase PDB id
Protein chains
(+ 0 more) 242 a.a. *
166 a.a. *
Waters ×177
* Residue conservation analysis
PDB id:
Name: Transferase
Title: 23s ribosomal RNA g2251 2'o-methyltransferase rlmb
Structure: Hypothetical tRNA/rrna methyltransferase yjfh. Chain: a, b, c, d, e, f, g, h. Synonym: methyltransferase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: mc1061 p3. Atcc: 47035. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
2.5Å     R-factor:   0.231     R-free:   0.279
Authors: G.Michel,M.Cygler
Key ref:
G.Michel et al. (2002). The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot. Structure, 10, 1303-1315. PubMed id: 12377117
03-May-02     Release date:   17-Oct-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P63177  (RLMB_ECOLI) -  23S rRNA (guanosine-2'-O-)-methyltransferase RlmB
243 a.a.
242 a.a.
Protein chains
Pfam   ArchSchema ?
P63177  (RLMB_ECOLI) -  23S rRNA (guanosine-2'-O-)-methyltransferase RlmB
243 a.a.
166 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.  - 23S rRNA (guanosine(2251)-2'-O)-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + guanosine2251 in 23S rRNA = S-adenosyl-L- homocysteine + 2'-O-methylguanosine2251 in 23S rRNA
+ guanosine(2251) in 23S rRNA
= S-adenosyl-L- homocysteine
+ 2'-O-methylguanosine(2251) in 23S rRNA
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     transferase activity     5 terms  


    Added reference    
Structure 10:1303-1315 (2002)
PubMed id: 12377117  
The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot.
G.Michel, V.Sauvé, R.Larocque, Y.Li, A.Matte, M.Cygler.
In Escherichia coli, RlmB catalyzes the methylation of guanosine 2251, a modification conserved in the peptidyltransferase domain of 23S rRNA. The crystal structure of this 2'O-methyltransferase has been determined at 2.5 A resolution. RlmB consists of an N-terminal domain connected by a flexible extended linker to a catalytic C-terminal domain and forms a dimer in solution. The C-terminal domain displays a divergent methyltransferase fold with a unique knotted region, and lacks the classic AdoMet binding site features. The N-terminal domain is similar to ribosomal proteins L7 and L30, suggesting a role in 23S rRNA recognition. The conserved residues in this novel family of 2'O-methyltransferases cluster in the knotted region, suggesting the location of the catalytic and AdoMet binding sites.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
  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.  
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.  
18163700 M.L.Mansfield (2007).
Efficient knot group identification as a tool for studying entanglements of polymers.
  J Chem Phys, 127, 244901.  
17368671 S.Wallin, K.B.Zeldovich, and E.I.Shakhnovich (2007).
The folding mechanics of a knotted protein.
  J Mol Biol, 368, 884-893.  
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.  
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.  
15906321 A.J.Bordner, and R.Abagyan (2005).
Statistical analysis and prediction of protein-protein interfaces.
  Proteins, 60, 353-366.  
  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.  
15195996 A.Dong, L.Zhou, X.Zhang, S.Stickel, R.J.Roberts, and X.Cheng (2004).
Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions.
  Biol Chem, 385, 373-379.
PDB code: 1svu
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.  
12837772 A.Matte, J.Sivaraman, I.Ekiel, K.Gehring, Z.Jia, and M.Cygler (2003).
Contribution of structural genomics to understanding the biology of Escherichia coli.
  J Bacteriol, 185, 3994-4002.  
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.  
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.  
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 code is shown on the right.