Compilation and analysis of intein sequences

Abstract

We have compiled a list of all the inteins (protein splicing elements) whose sequences have been published or were available from on-line sequence databases as of September 18, 1996. Analysis of the 36 available intein sequences refines the previously described intein motifs and reveals the presence of another intein motif, Block H. Furthermore, analysis of the new inteins reshapes our view of the conserved splice junction residues, since three inteins lack the intein penultimate His seen in prior examples. Comparison of intein sequences suggests that, in general, (i) inteins present in the same location within extein homologs from different organisms are very closely related to each other in paired sequence comparison or phylogenetic analysis and we suggest that they should be considered intein alleles; (ii) multiple inteins present in the same gene are no more similar to each other than to inteins present in different genes; (iii) phylogenetic analysis indicates that inteins are so divergent that trees with statistically significant branches cannot be generated except for intein alleles.

The Deinococcus radiodurans Snf2 intein caught in the act: Detection of the Class 3 intein signature Block F branched intermediate

“…5 Asp is not commonly found at B:7 although it is present in a few other inteins. [1][2][3][4][5] Mutation of Asp61 to Ala inhibited reactions at the N-terminal splice junction reducing the amount of spliced products and increasing the amount of C-terminal cleavage products [ Fig. 4(B) and Table II].…”

“…1). [2][3][4][5] Intein residues are referred to using the Block letter and the Block position separated by a colon.…”

“…1). [1][2][3][4][5] Two variations in the intein-mediated protein splicing mechanism were previously described, which involve direct attack on an amide bond at the N-terminal splice junction to generate a BI. [5][6][7]12,13 In Class 2 inteins, exemplified by the Methanococcus jannaschii (Mja) KlbA intein, 12,13 the Block G BI (III) is formed by nucleophilic attack of Cysþ1 on the peptide bond at the N-terminal splice junction (Fig.…”

“…1) and the mechanistic roles that they play. [1][2][3][4][5][6][7] Putative Class 3 inteins can be identified by class-specific sequence features: (a) the absence of a Cys, Ser, or Thr N-terminal nucleophile at A:1, (b) a noncontiguous WCT triplet at B:12, F:4, and G:5, and (c) Thrþ1 or Serþ1 as the first C-extein residue at G:8 instead of the more common Cysþ1 (Fig. 1).…”

“…Conserved positions are populated by groups of residues that have similar properties except for the Block B His (B:10), which is almost invariant. [1][2][3][4][5] An exemplary sequence is shown for each intein class. The most common residue found at selected positions is underlined and the common variations for these positions are shown.…”