Limits...
RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.

Bujnicki JM, Rychlewski L - BMC Bioinformatics (2002)

Bottom Line: Based on the results of sequence analysis and structure prediction, the residues involved in cofactor binding, target recognition and catalysis were identified, and the mechanism of the guanine-N2 methyltransfer reaction was proposed.Using the known Mj0882 structure, a comprehensive analysis of sequence-structure-function relationships in the family of genuine and putative m2G MTases was performed.The results provide novel insight into the mechanism of m2G methylation and will serve as a platform for experimental analysis of numerous uncharacterized N-MTases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Laboratory, International Institute of Cell and Molecular Biology, ul, ks, Trojdena 4, 02-109 Warsaw, Poland. iamb@wp.pl

ABSTRACT

Background: Escherichia coli guanine-N2 (m2G) methyltransferases (MTases) RsmC and RsmD modify nucleosides G1207 and G966 of 16S rRNA. They possess a common MTase domain in the C-terminus and a variable region in the N-terminus. Their C-terminal domain is related to the YbiN family of hypothetical MTases, but nothing is known about the structure or function of the N-terminal domain.

Results: Using a combination of sequence database searches and fold recognition methods it has been demonstrated that the N-termini of RsmC and RsmD are related to each other and that they represent a "degenerated" version of the C-terminal MTase domain. Novel members of the YbiN family from Archaea and Eukaryota were also indentified. It is inferred that YbiN and both domains of RsmC and RsmD are closely related to a family of putative MTases from Gram-positive bacteria and Archaea, typified by the Mj0882 protein from M. jannaschii (1dus in PDB). Based on the results of sequence analysis and structure prediction, the residues involved in cofactor binding, target recognition and catalysis were identified, and the mechanism of the guanine-N2 methyltransfer reaction was proposed.

Conclusions: Using the known Mj0882 structure, a comprehensive analysis of sequence-structure-function relationships in the family of genuine and putative m2G MTases was performed. The results provide novel insight into the mechanism of m2G methylation and will serve as a platform for experimental analysis of numerous uncharacterized N-MTases.

Show MeSH

Related in: MedlinePlus

Molecular surface of Mj0882 colored by the conservation score. The score have been calculated using SWISS-PDB VIEWER [54] based on superposition of 1dus coordinates with homology models of YbiN and the CTD of RsmC and RsmD (all proteins from E. coli). The color scale varies from blue to yellow, with invariant residues in blue and most variable in yellow. The docked AdoMet and guanine moieties are shown in wireframe representation.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC102759&req=5

Figure 5: Molecular surface of Mj0882 colored by the conservation score. The score have been calculated using SWISS-PDB VIEWER [54] based on superposition of 1dus coordinates with homology models of YbiN and the CTD of RsmC and RsmD (all proteins from E. coli). The color scale varies from blue to yellow, with invariant residues in blue and most variable in yellow. The docked AdoMet and guanine moieties are shown in wireframe representation.

Mentions: Although the presented docking model of Mj0882 complexed with AdoMet and guanine should be regarded as preliminary, it provides a useful platform for correlating the structure with sequence conservation in the Mj0882/RsmD/RsmC/YbiN family. The predicted AdoMet- and ribose-binding Asp residues (see above), as well as other invariant and highly conserved surface-exposed residues, map in the vicinity of the docked ligands, strongly supporting the model (Figure 5). The N2 group of the docked guanine is hydrogen bonded to the side chain of N129 and the carbonyl oxygen of P130. This is similar to the contacts made by the N6 group of the target adenine in the co-crystal structure of M.TaqI [29], which served as a docking template. As proposed for M.TaqI, these interactions could increase electron density of N2, change its hybridization from sp2 towards sp3, where the lone pair of N6 is no longer conjugated with the aromatic system, and thus contribute to its activation for nucleophilic attack on the activated methyl group of AdoMet. From the Mj0882 structure it is not obvious which residue may be responsible for eliminating the proton from the methylated N2 amine. The only conserved acidic residue in the vicinity of the active site corresponds to D41, and its localization is incompatible with the localization of the protons on N2 in the above-mentioned mechanism. If no massive conformational change of the m2G MTase occurs during RNA binding and catalysis, we propose that the proton is transferred directly to a bulk solvent molecule. In M.TaqI, the target base forms a face-to-face π-stacking interaction with Y108 from the NPPY tetrapeptide and a hydrophobic interaction with V21 from motif X. In Mj0882 these contacts are reversed (i.e. in motif IV Y108 is substituted by non-aromatic I and V21 is replaced by aromatic F35). Interestingly, all members of families RsmC, RsmD, and YbiN possess aromatic residues at both positions (Figure 1). It has been hypothesized that the methyltransfer reaction in N-MTases proceeds via a positively charged intermediate, which could be stabilized by cation-Ti interactions [30]. In m2G MTases, the electron-rich aromatic rings on both sides of the target could contribute to such stabilization.


RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.

Bujnicki JM, Rychlewski L - BMC Bioinformatics (2002)

Molecular surface of Mj0882 colored by the conservation score. The score have been calculated using SWISS-PDB VIEWER [54] based on superposition of 1dus coordinates with homology models of YbiN and the CTD of RsmC and RsmD (all proteins from E. coli). The color scale varies from blue to yellow, with invariant residues in blue and most variable in yellow. The docked AdoMet and guanine moieties are shown in wireframe representation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC102759&req=5

Figure 5: Molecular surface of Mj0882 colored by the conservation score. The score have been calculated using SWISS-PDB VIEWER [54] based on superposition of 1dus coordinates with homology models of YbiN and the CTD of RsmC and RsmD (all proteins from E. coli). The color scale varies from blue to yellow, with invariant residues in blue and most variable in yellow. The docked AdoMet and guanine moieties are shown in wireframe representation.
Mentions: Although the presented docking model of Mj0882 complexed with AdoMet and guanine should be regarded as preliminary, it provides a useful platform for correlating the structure with sequence conservation in the Mj0882/RsmD/RsmC/YbiN family. The predicted AdoMet- and ribose-binding Asp residues (see above), as well as other invariant and highly conserved surface-exposed residues, map in the vicinity of the docked ligands, strongly supporting the model (Figure 5). The N2 group of the docked guanine is hydrogen bonded to the side chain of N129 and the carbonyl oxygen of P130. This is similar to the contacts made by the N6 group of the target adenine in the co-crystal structure of M.TaqI [29], which served as a docking template. As proposed for M.TaqI, these interactions could increase electron density of N2, change its hybridization from sp2 towards sp3, where the lone pair of N6 is no longer conjugated with the aromatic system, and thus contribute to its activation for nucleophilic attack on the activated methyl group of AdoMet. From the Mj0882 structure it is not obvious which residue may be responsible for eliminating the proton from the methylated N2 amine. The only conserved acidic residue in the vicinity of the active site corresponds to D41, and its localization is incompatible with the localization of the protons on N2 in the above-mentioned mechanism. If no massive conformational change of the m2G MTase occurs during RNA binding and catalysis, we propose that the proton is transferred directly to a bulk solvent molecule. In M.TaqI, the target base forms a face-to-face π-stacking interaction with Y108 from the NPPY tetrapeptide and a hydrophobic interaction with V21 from motif X. In Mj0882 these contacts are reversed (i.e. in motif IV Y108 is substituted by non-aromatic I and V21 is replaced by aromatic F35). Interestingly, all members of families RsmC, RsmD, and YbiN possess aromatic residues at both positions (Figure 1). It has been hypothesized that the methyltransfer reaction in N-MTases proceeds via a positively charged intermediate, which could be stabilized by cation-Ti interactions [30]. In m2G MTases, the electron-rich aromatic rings on both sides of the target could contribute to such stabilization.

Bottom Line: Based on the results of sequence analysis and structure prediction, the residues involved in cofactor binding, target recognition and catalysis were identified, and the mechanism of the guanine-N2 methyltransfer reaction was proposed.Using the known Mj0882 structure, a comprehensive analysis of sequence-structure-function relationships in the family of genuine and putative m2G MTases was performed.The results provide novel insight into the mechanism of m2G methylation and will serve as a platform for experimental analysis of numerous uncharacterized N-MTases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Laboratory, International Institute of Cell and Molecular Biology, ul, ks, Trojdena 4, 02-109 Warsaw, Poland. iamb@wp.pl

ABSTRACT

Background: Escherichia coli guanine-N2 (m2G) methyltransferases (MTases) RsmC and RsmD modify nucleosides G1207 and G966 of 16S rRNA. They possess a common MTase domain in the C-terminus and a variable region in the N-terminus. Their C-terminal domain is related to the YbiN family of hypothetical MTases, but nothing is known about the structure or function of the N-terminal domain.

Results: Using a combination of sequence database searches and fold recognition methods it has been demonstrated that the N-termini of RsmC and RsmD are related to each other and that they represent a "degenerated" version of the C-terminal MTase domain. Novel members of the YbiN family from Archaea and Eukaryota were also indentified. It is inferred that YbiN and both domains of RsmC and RsmD are closely related to a family of putative MTases from Gram-positive bacteria and Archaea, typified by the Mj0882 protein from M. jannaschii (1dus in PDB). Based on the results of sequence analysis and structure prediction, the residues involved in cofactor binding, target recognition and catalysis were identified, and the mechanism of the guanine-N2 methyltransfer reaction was proposed.

Conclusions: Using the known Mj0882 structure, a comprehensive analysis of sequence-structure-function relationships in the family of genuine and putative m2G MTases was performed. The results provide novel insight into the mechanism of m2G methylation and will serve as a platform for experimental analysis of numerous uncharacterized N-MTases.

Show MeSH
Related in: MedlinePlus