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

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.


Superimposed local structures around the four S···O interactions and one S···N interaction observed in PLA2-DG. Pictures were drawn using the structural data of PDB (Table 1) with dS···X≤0.05 Å. The sulfur, oxygen, nitrogen, and carbon atoms are shown in yellow, red, blue, and black, respectively. The residue numbers of bovine PLA2 are indicated. For porcine and human PLA2, the residue numbers may be different (see the footnotes of Table 1). (A) The S(C44)···O(D40) interaction. (B) The S(C61)···O(A55) interaction. The structures of human PLA2 [1LE6(A) and 1LE6(B)] are omitted because they are significantly deviated. (C) The S(C84)···O(C96) interaction. (D) The S(C98)···O(F94) interaction. (E) The S(M8)···N(R100) interaction.
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f2-2_23: Superimposed local structures around the four S···O interactions and one S···N interaction observed in PLA2-DG. Pictures were drawn using the structural data of PDB (Table 1) with dS···X≤0.05 Å. The sulfur, oxygen, nitrogen, and carbon atoms are shown in yellow, red, blue, and black, respectively. The residue numbers of bovine PLA2 are indicated. For porcine and human PLA2, the residue numbers may be different (see the footnotes of Table 1). (A) The S(C44)···O(D40) interaction. (B) The S(C61)···O(A55) interaction. The structures of human PLA2 [1LE6(A) and 1LE6(B)] are omitted because they are significantly deviated. (C) The S(C84)···O(C96) interaction. (D) The S(C98)···O(F94) interaction. (E) The S(M8)···N(R100) interaction.

Mentions: As shown in Table 1, four S···O interactions and one S···N interaction were commonly observed for PLA2-DG. The bold-style numbers of the relative distance dS···X in the table indicate strong S···X (X=O and N) interactions with d≤0.1 Å. It should be noted that none of these common interactions were detected for 1GH4. This must be because the three lysine residues (K56, K120, and K121) have been mutated with three methionine residues, which would destabilize the three-dimensional structure significantly. Local structures around the five common S···X interactions are shown in Fig. 2.


Possible roles of S · · · O and S · · · N interactions in the functions and evolution of phospholipase A 2
Superimposed local structures around the four S···O interactions and one S···N interaction observed in PLA2-DG. Pictures were drawn using the structural data of PDB (Table 1) with dS···X≤0.05 Å. The sulfur, oxygen, nitrogen, and carbon atoms are shown in yellow, red, blue, and black, respectively. The residue numbers of bovine PLA2 are indicated. For porcine and human PLA2, the residue numbers may be different (see the footnotes of Table 1). (A) The S(C44)···O(D40) interaction. (B) The S(C61)···O(A55) interaction. The structures of human PLA2 [1LE6(A) and 1LE6(B)] are omitted because they are significantly deviated. (C) The S(C84)···O(C96) interaction. (D) The S(C98)···O(F94) interaction. (E) The S(M8)···N(R100) interaction.
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Related In: Results  -  Collection

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f2-2_23: Superimposed local structures around the four S···O interactions and one S···N interaction observed in PLA2-DG. Pictures were drawn using the structural data of PDB (Table 1) with dS···X≤0.05 Å. The sulfur, oxygen, nitrogen, and carbon atoms are shown in yellow, red, blue, and black, respectively. The residue numbers of bovine PLA2 are indicated. For porcine and human PLA2, the residue numbers may be different (see the footnotes of Table 1). (A) The S(C44)···O(D40) interaction. (B) The S(C61)···O(A55) interaction. The structures of human PLA2 [1LE6(A) and 1LE6(B)] are omitted because they are significantly deviated. (C) The S(C84)···O(C96) interaction. (D) The S(C98)···O(F94) interaction. (E) The S(M8)···N(R100) interaction.
Mentions: As shown in Table 1, four S···O interactions and one S···N interaction were commonly observed for PLA2-DG. The bold-style numbers of the relative distance dS···X in the table indicate strong S···X (X=O and N) interactions with d≤0.1 Å. It should be noted that none of these common interactions were detected for 1GH4. This must be because the three lysine residues (K56, K120, and K121) have been mutated with three methionine residues, which would destabilize the three-dimensional structure significantly. Local structures around the five common S···X interactions are shown in Fig. 2.

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.