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Possible roles of S · · · O and S · · · N interactions in the functions and evolution of phospholipase A 2

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ABSTRACT

To investigate possible roles of S···X (X= O, N, S) interactions in the functions and evolution of a protein, two types of database analyses were carried out for a vertebrate phospholipase A2 (PLA2) family. A comprehensive search for close S···X contacts in the structures retrieved from protein data bank (PDB) revealed that there are four common S···O interactions and one common S···N interaction for the PLA2 domain group (PLA2-DG), while an additional three S···O interactions were found for the snake PLA2 domain group (sPLA2-DG). On the other hand, a phylogenetic analysis on the conservation of the observed S···O and S···N interactions over various amino acid sequences of sPLA2-DG demonstrated probable clustering of the interactions on the dendrogram. Most of the interactions characterized for PLA2 were found to reside in the vicinity of the active site and to be able to tolerate the conformational changes due to the substrate binding. These observations suggested that the S···X interactions play some role in the functions and evolution of the PLA2 family.

No MeSH data available.


Superimposed local structures around the three S···O interactions additionally found in sPLA2-DG. Pictures were drawn using the structural data of PDB (Table 2) with dS···O≤0.10 Å. The sulfur, oxygen, nitrogen, and carbon atoms are shown in yellow, red, blue, and black, respectively. The residue numbers of Russell’s viper (r. viper) PLA2 are indicated. For the other snake PLA2, the residue numbers may be different (see the footnotes of Table 2). (A) The S(C27)···O(R36) interaction. (B) The S(C44)···O(C105) interaction shown with the bifurcated S(C44)···O(A40) interaction. (C) The S(C50)···O(F46) interaction.
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f3-2_23: Superimposed local structures around the three S···O interactions additionally found in sPLA2-DG. Pictures were drawn using the structural data of PDB (Table 2) with dS···O≤0.10 Å. The sulfur, oxygen, nitrogen, and carbon atoms are shown in yellow, red, blue, and black, respectively. The residue numbers of Russell’s viper (r. viper) PLA2 are indicated. For the other snake PLA2, the residue numbers may be different (see the footnotes of Table 2). (A) The S(C27)···O(R36) interaction. (B) The S(C44)···O(C105) interaction shown with the bifurcated S(C44)···O(A40) interaction. (C) The S(C50)···O(F46) interaction.

Mentions: Fig. 3 shows superimposed local structures around the S(C27)···O(R36), S(C44)···O(C105), and S(C50)···O(F46) interactions that were found in sPLA2-DG in addition to the five interactions common to PLA2-DG.


Possible roles of S · · · O and S · · · N interactions in the functions and evolution of phospholipase A 2
Superimposed local structures around the three S···O interactions additionally found in sPLA2-DG. Pictures were drawn using the structural data of PDB (Table 2) with dS···O≤0.10 Å. The sulfur, oxygen, nitrogen, and carbon atoms are shown in yellow, red, blue, and black, respectively. The residue numbers of Russell’s viper (r. viper) PLA2 are indicated. For the other snake PLA2, the residue numbers may be different (see the footnotes of Table 2). (A) The S(C27)···O(R36) interaction. (B) The S(C44)···O(C105) interaction shown with the bifurcated S(C44)···O(A40) interaction. (C) The S(C50)···O(F46) interaction.
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Related In: Results  -  Collection

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f3-2_23: Superimposed local structures around the three S···O interactions additionally found in sPLA2-DG. Pictures were drawn using the structural data of PDB (Table 2) with dS···O≤0.10 Å. The sulfur, oxygen, nitrogen, and carbon atoms are shown in yellow, red, blue, and black, respectively. The residue numbers of Russell’s viper (r. viper) PLA2 are indicated. For the other snake PLA2, the residue numbers may be different (see the footnotes of Table 2). (A) The S(C27)···O(R36) interaction. (B) The S(C44)···O(C105) interaction shown with the bifurcated S(C44)···O(A40) interaction. (C) The S(C50)···O(F46) interaction.
Mentions: Fig. 3 shows superimposed local structures around the S(C27)···O(R36), S(C44)···O(C105), and S(C50)···O(F46) interactions that were found in sPLA2-DG in addition to the five interactions common to PLA2-DG.

View Article: PubMed Central - PubMed

ABSTRACT

To investigate possible roles of S···X (X= O, N, S) interactions in the functions and evolution of a protein, two types of database analyses were carried out for a vertebrate phospholipase A2 (PLA2) family. A comprehensive search for close S···X contacts in the structures retrieved from protein data bank (PDB) revealed that there are four common S···O interactions and one common S···N interaction for the PLA2 domain group (PLA2-DG), while an additional three S···O interactions were found for the snake PLA2 domain group (sPLA2-DG). On the other hand, a phylogenetic analysis on the conservation of the observed S···O and S···N interactions over various amino acid sequences of sPLA2-DG demonstrated probable clustering of the interactions on the dendrogram. Most of the interactions characterized for PLA2 were found to reside in the vicinity of the active site and to be able to tolerate the conformational changes due to the substrate binding. These observations suggested that the S···X interactions play some role in the functions and evolution of the PLA2 family.

No MeSH data available.