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Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.

Kurowski MA, Sasin JM, Feder M, Debski J, Bujnicki JM - BMC Bioinformatics (2003)

Bottom Line: We analyzed the sequence divergence in two distinct lineages of the SPOUT superfamily in the context of surface features and preferred cofactor binding mode to propose specific function for the conserved residues.In the vicinity of the cofactor-binding site, subfamily-conserved grooves were identified on the protein surface, suggesting location of the target-binding/catalytic site.Functionally important residues were inferred and a general reaction mechanism, involving conformational change of a glycine-rich loop, was proposed.

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Affiliation: Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland. michal@genesilico.pl

ABSTRACT

Background: There are several evolutionarily unrelated and structurally dissimilar superfamilies of S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTases). A new superfamily (SPOUT) has been recently characterized on a sequence level and three structures of its members (1gz0, 1ipa, and 1k3r) have been solved. However, none of these structures include the cofactor or the substrate. Due to the strong evolutionary divergence and the paucity of experimental information, no confident predictions of protein-ligand and protein-substrate interactions could be made, which hampered the study of sequence-structure-function relationships in the SPOUT superfamily.

Results: We used the computational docking program AutoDock to identify the AdoMet-binding site on the surface of three MTase structures. We analyzed the sequence divergence in two distinct lineages of the SPOUT superfamily in the context of surface features and preferred cofactor binding mode to propose specific function for the conserved residues.

Conclusion: Our docking analysis has confidently predicted the common AdoMet-binding site in three remotely related proteins structures. In the vicinity of the cofactor-binding site, subfamily-conserved grooves were identified on the protein surface, suggesting location of the target-binding/catalytic site. Functionally important residues were inferred and a general reaction mechanism, involving conformational change of a glycine-rich loop, was proposed.

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Lowest-energy docking solutions obtained for a) 1gz0, b) 1ipa, c) 1k3r. AdoMet and selected important residues are shown in the wireframe representation and labeled. The label for the invariant Arg side chain, provided by the second monomer, is boxed. The rest of the protein is shown in a schematic representation (brown helices, green strands and purple loops). Selected sidechains are colored according to their physicochemical properties (Arg and Lys – blue; Glu – red; Thr and Ser – green; aliphatic (Pro, Val, Leu) – gray; Gly – cyan). For the residues that bind the cofactor and for the cofactor itself, the following color scheme is used: C – white, O – red, N – blue, S – yellow). Predicted hydrogen bonds are shown as green broken lines.
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Figure 4: Lowest-energy docking solutions obtained for a) 1gz0, b) 1ipa, c) 1k3r. AdoMet and selected important residues are shown in the wireframe representation and labeled. The label for the invariant Arg side chain, provided by the second monomer, is boxed. The rest of the protein is shown in a schematic representation (brown helices, green strands and purple loops). Selected sidechains are colored according to their physicochemical properties (Arg and Lys – blue; Glu – red; Thr and Ser – green; aliphatic (Pro, Val, Leu) – gray; Gly – cyan). For the residues that bind the cofactor and for the cofactor itself, the following color scheme is used: C – white, O – red, N – blue, S – yellow). Predicted hydrogen bonds are shown as green broken lines.

Mentions: Figure 3 shows the populations of 20 lowest-energy docking solutions for all three structures, as obtained in the course of the LGA search. The values of the estimated energy of protein-ligand interactions for the best docking solutions are summarized in Table 2; the ligand-binding pockets of 1gz0, 1ipa, and 1k3r are shown in Figure 4. According to the results of our docking simulations, AdoMet binds to all SPOUT MTases in the same folded conformation, similar to that observed for AdoHcy in unrelated CbiF and SET MTases, and different from the extended conformation typical for the RFM superfamily (Figure 1). Nevertheless, in all "top 20" solutions for each SPOUT MTase, the ribose moiety of AdoMet is in the C2'-endo conformation, similarly to the RFM structures, while in CbiF it is C3'-endo (1cbf) and in the SET superfamily C1'-exo (Set79; 1mt6) or C2'-exo (Rubisco LSMT; 1mlv). In nearly all low-energy docking solutions, the cofactor adopts an anti conformation about the glycosidic bond (typical for all MTase structures solved to date (Figure 1; review: [6]), which maximizes the burial of the adenine moiety (Figure 3).


Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.

Kurowski MA, Sasin JM, Feder M, Debski J, Bujnicki JM - BMC Bioinformatics (2003)

Lowest-energy docking solutions obtained for a) 1gz0, b) 1ipa, c) 1k3r. AdoMet and selected important residues are shown in the wireframe representation and labeled. The label for the invariant Arg side chain, provided by the second monomer, is boxed. The rest of the protein is shown in a schematic representation (brown helices, green strands and purple loops). Selected sidechains are colored according to their physicochemical properties (Arg and Lys – blue; Glu – red; Thr and Ser – green; aliphatic (Pro, Val, Leu) – gray; Gly – cyan). For the residues that bind the cofactor and for the cofactor itself, the following color scheme is used: C – white, O – red, N – blue, S – yellow). Predicted hydrogen bonds are shown as green broken lines.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC153507&req=5

Figure 4: Lowest-energy docking solutions obtained for a) 1gz0, b) 1ipa, c) 1k3r. AdoMet and selected important residues are shown in the wireframe representation and labeled. The label for the invariant Arg side chain, provided by the second monomer, is boxed. The rest of the protein is shown in a schematic representation (brown helices, green strands and purple loops). Selected sidechains are colored according to their physicochemical properties (Arg and Lys – blue; Glu – red; Thr and Ser – green; aliphatic (Pro, Val, Leu) – gray; Gly – cyan). For the residues that bind the cofactor and for the cofactor itself, the following color scheme is used: C – white, O – red, N – blue, S – yellow). Predicted hydrogen bonds are shown as green broken lines.
Mentions: Figure 3 shows the populations of 20 lowest-energy docking solutions for all three structures, as obtained in the course of the LGA search. The values of the estimated energy of protein-ligand interactions for the best docking solutions are summarized in Table 2; the ligand-binding pockets of 1gz0, 1ipa, and 1k3r are shown in Figure 4. According to the results of our docking simulations, AdoMet binds to all SPOUT MTases in the same folded conformation, similar to that observed for AdoHcy in unrelated CbiF and SET MTases, and different from the extended conformation typical for the RFM superfamily (Figure 1). Nevertheless, in all "top 20" solutions for each SPOUT MTase, the ribose moiety of AdoMet is in the C2'-endo conformation, similarly to the RFM structures, while in CbiF it is C3'-endo (1cbf) and in the SET superfamily C1'-exo (Set79; 1mt6) or C2'-exo (Rubisco LSMT; 1mlv). In nearly all low-energy docking solutions, the cofactor adopts an anti conformation about the glycosidic bond (typical for all MTase structures solved to date (Figure 1; review: [6]), which maximizes the burial of the adenine moiety (Figure 3).

Bottom Line: We analyzed the sequence divergence in two distinct lineages of the SPOUT superfamily in the context of surface features and preferred cofactor binding mode to propose specific function for the conserved residues.In the vicinity of the cofactor-binding site, subfamily-conserved grooves were identified on the protein surface, suggesting location of the target-binding/catalytic site.Functionally important residues were inferred and a general reaction mechanism, involving conformational change of a glycine-rich loop, was proposed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland. michal@genesilico.pl

ABSTRACT

Background: There are several evolutionarily unrelated and structurally dissimilar superfamilies of S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTases). A new superfamily (SPOUT) has been recently characterized on a sequence level and three structures of its members (1gz0, 1ipa, and 1k3r) have been solved. However, none of these structures include the cofactor or the substrate. Due to the strong evolutionary divergence and the paucity of experimental information, no confident predictions of protein-ligand and protein-substrate interactions could be made, which hampered the study of sequence-structure-function relationships in the SPOUT superfamily.

Results: We used the computational docking program AutoDock to identify the AdoMet-binding site on the surface of three MTase structures. We analyzed the sequence divergence in two distinct lineages of the SPOUT superfamily in the context of surface features and preferred cofactor binding mode to propose specific function for the conserved residues.

Conclusion: Our docking analysis has confidently predicted the common AdoMet-binding site in three remotely related proteins structures. In the vicinity of the cofactor-binding site, subfamily-conserved grooves were identified on the protein surface, suggesting location of the target-binding/catalytic site. Functionally important residues were inferred and a general reaction mechanism, involving conformational change of a glycine-rich loop, was proposed.

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