The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot.

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.

[1]  J. Bujnicki,et al.  Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda2 protein , 2001, Genome Biology.

[2]  Richard A. Dixon,et al.  Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases , 2001, Nature Structural Biology.

[3]  P. Mitchell,et al.  Methylation sites in Escherichia coli ribosomal RNA: localization and identification of four new sites of methylation in 23S rRNA. , 1992, Biochemistry.

[4]  J. Thompson,et al.  Resistance to thiostrepton, siomycin, and sporangiomycin in actinomycetes that produce them , 1980, Journal of bacteriology.

[5]  J Navaza,et al.  Implementation of molecular replacement in AMoRe. , 2001, Acta crystallographica. Section D, Biological crystallography.

[6]  Marc L. Mansfield,et al.  Fit to be tied , 1997, Nature Structural Biology.

[7]  Patrice Gouet,et al.  ESPript: analysis of multiple sequence alignments in PostScript , 1999, Bioinform..

[8]  E A Merritt,et al.  Raster3D: photorealistic molecular graphics. , 1997, Methods in enzymology.

[9]  Ann M Stock,et al.  Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine. , 1997, Structure.

[10]  Marc L. Mansfield,et al.  Knots in Hamilton Cycles , 1994 .

[11]  William R. Taylor,et al.  A deeply knotted protein structure and how it might fold , 2000, Nature.

[12]  Ohta Toshio,et al.  Analysis of the self-defense gene (fmrO) of a fortimicin A (astromicin) producer, Micromonospora olivasterospora: comparison with other aminoglycoside-resistance-encoding genes. , 1993 .

[13]  C. Chothia,et al.  The atomic structure of protein-protein recognition sites. , 1999, Journal of molecular biology.

[14]  Jean M. Severin,et al.  Solution structure of an rRNA methyltransferase (ErmAM) that confers macrolide-lincosamide-streptogramin antibiotic resistance , 1997, Nature Structural Biology.

[15]  P. Wikström,et al.  The rlmB Gene Is Essential for Formation of Gm2251 in 23S rRNA but Not for Ribosome Maturation inEscherichia coli , 2001, Journal of bacteriology.

[16]  Keith S. Wilson,et al.  The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase , 1998, Nature Structural Biology.

[17]  W. Lipscomb,et al.  The crystal structure of Haelll methyltransferase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing , 1995, Cell.

[18]  D. Santi,et al.  Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes. , 1996, Nucleic acids research.

[19]  A. Byström,et al.  Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine. , 1989, Science.

[20]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[21]  D Job,et al.  The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 Å resolution , 1997, The EMBO journal.

[22]  T. Steitz,et al.  The structural basis of ribosome activity in peptide bond synthesis. , 2000, Science.

[23]  G. Varani,et al.  Recent advances in RNA-protein recognition. , 2001, Current opinion in structural biology.

[24]  Eugene V Koonin,et al.  SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. , 2002, Journal of molecular microbiology and biotechnology.

[25]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[26]  J. Bachellerie,et al.  The yeast Saccharomyces cerevisiae YDL112w ORF encodes the putative 2'-O-ribose methyltransferase catalyzing the formation of Gm18 in tRNAs. , 1999, RNA.

[27]  Susan A. White,et al.  A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex , 1999, Nature Structural Biology.

[28]  S. Harrison,et al.  Structure of the reovirus core at 3.6 Å resolution , 2000, Nature.

[29]  Xiaodong Cheng,et al.  Crystal structure of the conserved core of protein arginine methyltransferase PRMT3 , 2000, The EMBO journal.

[30]  A. Bechthold,et al.  An ATP-Binding Cassette Transporter and Two rRNA Methyltransferases Are Involved in Resistance to Avilamycin in the Producer Organism Streptomyces viridochromogenesTü57 , 2001, Antimicrobial Agents and Chemotherapy.

[31]  B. Lane,et al.  In vivo incorporation of methyl groups into the ribose of Escherichia coli ribosomal RNA. , 1967, Journal of molecular biology.

[32]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[33]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[34]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[35]  R. Huber,et al.  Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12 , 2000, The EMBO journal.

[36]  W A Hendrickson,et al.  Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three‐dimensional structure. , 1990, The EMBO journal.

[37]  T. Steitz,et al.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.

[38]  C. Chothia,et al.  The structure of protein-protein recognition sites. , 1990, The Journal of biological chemistry.

[39]  F A Quiocho,et al.  Structural basis for sequence-nonspecific recognition of 5'-capped mRNA by a cap-modifying enzyme. , 1998, Molecular cell.

[40]  J. Ebel,et al.  Primary and secondary structures of Escherichia coli MRE 600 23S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast 23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs. , 1981, Nucleic acids research.

[41]  R L Walter,et al.  Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair. , 2000, Structure.

[42]  W. Saenger,et al.  Universal catalytic domain structure of AdoMet-dependent methyltransferases. , 1995, Journal of molecular biology.

[43]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[44]  Anders Liljas,et al.  Crystal structure of catechol O-methyltransferase , 1994, Nature.

[45]  W. Saenger,et al.  Three-dimensional structure of the adenine-specific DNA methyltransferase M.Taq I in complex with the cofactor S-adenosylmethionine. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[47]  Guoguang Lu,et al.  TOP: a new method for protein structure comparisons and similarity searches , 2000 .

[48]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[49]  T. Mason,et al.  Functional requirement of a site-specific ribose methylation in ribosomal RNA. , 1993, Science.

[50]  E. Fauman,et al.  RNA methylation under heat shock control. , 2000, Molecular cell.

[51]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[52]  C. Gustafsson,et al.  The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2'-O-methyltransferase activity. , 1997, Nucleic acids research.