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BMC Bioinformatics

, 7:305

First Online: 16 June 2006Received: 04 April 2006Accepted: 16 June 2006

Abstract

BackgroundREX1 and REX2 are protein components of the RNA editing complex the editosome and function as exouridylylases. The exact roles of REX1 and REX2 in the editosome are unclear and the consequences of the presence of two related proteins are not fully understood. Here, a variety of computational studies were performed to enhance understanding of the structure and function of REX proteins in Trypanosoma and Leishmania species.

ResultsSequence analysis and homology modeling of the Endonuclease-Exonuclease-Phosphatase EEP domain at the C-terminus of REX1 and REX2 highlights a common active site shared by all EEP domains. Phylogenetic analysis indicates that REX proteins contain a distinct subfamily of EEP domains. Inspection of three-dimensional models of the EEP domain in Trypanosoma brucei REX1 and REX2, and Leishmania major REX1 suggests variations of previously characterized key residues likely to be important in catalysis and determining substrate specificity.

ConclusionWe have identified features of the REX EEP domain that distinguish it from other family members and hence subfamily specific determinants of catalysis and substrate binding. The results provide specific guidance for experimental investigations about the roles of REX proteins in RNA editing.

AbbreviationsREXRNA editing exouridylylase

EEPEndonuclease-Exonuclease-Phosphatase

RENRNA editing endonuclease

RETRNA editing terminal uridylyl transferase

TUTaseterminal uridylyl transferase

exoUaseexouridylylase

RELRNA editing ligase

REHRNA editing helicase, APE, apurinic-apyrimidinic endonuclease

OBoligonucleotide binding

L1-ENL1 endonuclease

ExoIIIexonuclease III

I5PPinositol polyphosphate 5-phosphatase

pol IDNA polymerase I

pol βDNA polymerase β.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-7-305 contains supplementary material, which is available to authorized users.

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Author: I Saira Mian - Elizabeth A Worthey - Reza Salavati

Source: https://link.springer.com/



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