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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.

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The docking model of AdoMet and guanosine to the Mj0882 structure. Residues predicted to participate in cofactor and target binding are shown in wireframe representation and are labeled in cyan and in green, respectively.
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Figure 3: The docking model of AdoMet and guanosine to the Mj0882 structure. Residues predicted to participate in cofactor and target binding are shown in wireframe representation and are labeled in cyan and in green, respectively.

Mentions: In order to dock the AdoMet molecule to the 1dus coordinates, we sought to identify those MTase structures, which display greatest similarity to the Mj0882 structure in the cofactor-binding region. VAST and DALI searches confirmed that the region spanning residues 55 to 117 in the Mj0882 sequence is the most similar to MTases that modify hydroxyl groups (data not shown), as well as the entire protein structure (see above). The catechol O-MTase structure (COMT) [26](1vid) was reported as the best hit by VAST (Score 7.1, RMSD 1.3). It was used as a structural template, because it was the only well-scored structure of a MTase complexed with AdoMet and not with its non-reactive analogs or the reaction product AdoHcy. Accordingly, the AdoMet moiety was copied from COMT to the Mj0882 structure based on superposition of the 1vid and 1dus coordinates. The obtained Mj0882-AdoMet complex showed no severe atomic overlaps and the cofactor seemed to fit the groove on the protein surface very well. According to AutoDock [27] the energy of the interactions between the 1dus structure and AdoMet in the docked complex is very favorable (-15.03 kcal/mol) even though it is lower from that calculated for the template COMT-AdoMet complex (-22.04 kcal/mol) in the 1vid structure [26]. From the docked model, in striking analogy to most MTase structures (reviewed in ref. [12]), the following three crucial contacts can be predicted: i) D61 from motif I coordinates the methionine amino group of AdoMet via an ordered water molecule. Even though the corresponding acidic residue is conserved in nearly all MTases analyzed to date, this contact has been identified only recently in the high-resolution structure of the RrmJ MTase [28]. ii) D84 from motif II coordinates the ribose hydroxyl groups, iii) D113 from motif III coordinates the amino group of the adenine moiety. Non-polar interactions between the side-chains of I85 and L114 and the adenine ring further contribute to the binding (Figure 3).


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)

The docking model of AdoMet and guanosine to the Mj0882 structure. Residues predicted to participate in cofactor and target binding are shown in wireframe representation and are labeled in cyan and in green, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: The docking model of AdoMet and guanosine to the Mj0882 structure. Residues predicted to participate in cofactor and target binding are shown in wireframe representation and are labeled in cyan and in green, respectively.
Mentions: In order to dock the AdoMet molecule to the 1dus coordinates, we sought to identify those MTase structures, which display greatest similarity to the Mj0882 structure in the cofactor-binding region. VAST and DALI searches confirmed that the region spanning residues 55 to 117 in the Mj0882 sequence is the most similar to MTases that modify hydroxyl groups (data not shown), as well as the entire protein structure (see above). The catechol O-MTase structure (COMT) [26](1vid) was reported as the best hit by VAST (Score 7.1, RMSD 1.3). It was used as a structural template, because it was the only well-scored structure of a MTase complexed with AdoMet and not with its non-reactive analogs or the reaction product AdoHcy. Accordingly, the AdoMet moiety was copied from COMT to the Mj0882 structure based on superposition of the 1vid and 1dus coordinates. The obtained Mj0882-AdoMet complex showed no severe atomic overlaps and the cofactor seemed to fit the groove on the protein surface very well. According to AutoDock [27] the energy of the interactions between the 1dus structure and AdoMet in the docked complex is very favorable (-15.03 kcal/mol) even though it is lower from that calculated for the template COMT-AdoMet complex (-22.04 kcal/mol) in the 1vid structure [26]. From the docked model, in striking analogy to most MTase structures (reviewed in ref. [12]), the following three crucial contacts can be predicted: i) D61 from motif I coordinates the methionine amino group of AdoMet via an ordered water molecule. Even though the corresponding acidic residue is conserved in nearly all MTases analyzed to date, this contact has been identified only recently in the high-resolution structure of the RrmJ MTase [28]. ii) D84 from motif II coordinates the ribose hydroxyl groups, iii) D113 from motif III coordinates the amino group of the adenine moiety. Non-polar interactions between the side-chains of I85 and L114 and the adenine ring further contribute to the binding (Figure 3).

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