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 electrostatic potential. The values of surface potential are expressed as a spectrum ranging from -5 kT/e (deep red) to +5 kT/e (deep blue). The docked AdoMet and guanine moieties are shown in wireframe representation.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC102759&req=5

Figure 6: Molecular surface of Mj0882 colored by the electrostatic potential. The values of surface potential are expressed as a spectrum ranging from -5 kT/e (deep red) to +5 kT/e (deep blue). The docked AdoMet and guanine moieties are shown in wireframe representation.

Mentions: The predicted guanine-binding mode implies that the target nucleotide is "flipped out" of the rRNA into the catalytic site, similarly to the mechanism discovered for DNA: m5C MTases [31] and extended to DNA N-MTases [29,32]. In bacterial 16S rRNA G966 and G1516 occur in extrahelical regions, which should facilitate their binding in the catalytic pocket of the enzyme, but G1207 is base-paired in the helix 34 stem [7]. The m2G1207 MTase RsmC reacts with the 30S ribosomal particles but barely at all with 16S RNA, while the m2G966 MTase RsmD requires only the S7 and S19 proteins to methylate its target in the 16S RNA [10]. It has been inferred that both these nucleotides are modified after the association of several ribosomal proteins with the 16S rRNA, which is likely to assume the native secondary structure, but before assembly of the 30S subunit is complete [10]. The positively charged surface of Mj0882 in the area next to the docked guanine suggests charge complementarity to the negatively charged phosphate groups in rRNA (Figure 6). It will be interesting to study the base-flipping capabilities of RsmC and RsmD, since they may shed the light on the evolution of presumed mechanistic differences between the nucleic acid MTases that flip their target out of the double helix and those modifying extrahelical bases.


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 electrostatic potential. The values of surface potential are expressed as a spectrum ranging from -5 kT/e (deep red) to +5 kT/e (deep blue). 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 6: Molecular surface of Mj0882 colored by the electrostatic potential. The values of surface potential are expressed as a spectrum ranging from -5 kT/e (deep red) to +5 kT/e (deep blue). The docked AdoMet and guanine moieties are shown in wireframe representation.
Mentions: The predicted guanine-binding mode implies that the target nucleotide is "flipped out" of the rRNA into the catalytic site, similarly to the mechanism discovered for DNA: m5C MTases [31] and extended to DNA N-MTases [29,32]. In bacterial 16S rRNA G966 and G1516 occur in extrahelical regions, which should facilitate their binding in the catalytic pocket of the enzyme, but G1207 is base-paired in the helix 34 stem [7]. The m2G1207 MTase RsmC reacts with the 30S ribosomal particles but barely at all with 16S RNA, while the m2G966 MTase RsmD requires only the S7 and S19 proteins to methylate its target in the 16S RNA [10]. It has been inferred that both these nucleotides are modified after the association of several ribosomal proteins with the 16S rRNA, which is likely to assume the native secondary structure, but before assembly of the 30S subunit is complete [10]. The positively charged surface of Mj0882 in the area next to the docked guanine suggests charge complementarity to the negatively charged phosphate groups in rRNA (Figure 6). It will be interesting to study the base-flipping capabilities of RsmC and RsmD, since they may shed the light on the evolution of presumed mechanistic differences between the nucleic acid MTases that flip their target out of the double helix and those modifying extrahelical bases.

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