A Dual Leucine-rich Repeat in Proteins from the Eukaryotic SAR Group

Author:

Matsushima Norio12,Batkhishig Dashdavaa3,Enkhbayar Purevjav4,Kretsinger Robert H.5

Affiliation:

1. Division of Bioinformatics, Institute of Tandem Repeats, Noboribetsu 059-0464, Japan

2. Center for Medical Education, Sapporo Medical University, Sapporo 060-8556, Japan

3. Department of Physics, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar 210648, Mongolia

4. Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia

5. Department of Biology, University of Virginia, Charlottesville, VA 22904, USA

Abstract

Background: Leucine-rich repeats (LRRs) occurring in tandem are 20 ⎼ 29 amino acids long. Eleven LRR types have been recognized; they include plant-specific (PS) type with the consensus of LxxLxLxxNxL SGxIPxxIxxLxx of 24 residues and SDS22-like type with the consensus of LxxLxLxxNxL xxIxxIxxLxx of 22 residues. Objective: A viral LRR protein in metagenome data indicated that most of the LRRs (5/6 = 0.83) are represented by the consensus of LxxLDLxxTxV SGKLSDLxxLTN of 23 residues. This LRR shows a dual characteristic of PS and SDS22-like LRRs (called PS/SDS22-like LRR). A comprehensive similarity search was performed under the hypothesis that many proteins contain LRR domains consisting of only or mainly PS/SDS22-like LRR. Methods: Sequence similarity search by the FASTA and BLAST programs was performed using the sequence of this PS/SDS22-like LRR domain as a query sequence. The presence of PS/SDS22-like LRR was screened within the LRR domains in known structures. Results: Over 280 LRR proteins were identified from protists, fungi, and bacteria; ~ 40% come from the SAR group (the phyla Alveolate and Stramenopiles). The secondary structure analysis of PS/SDS22-like LRRs occurring sporadically in the known structures indicates three or four type patterns of secondary structures. Conclusion: PS/SDS22-like LRR forms an LRR class with PS, SDS22-like and Leptospira-like LRRs. It appears that PS/SDS22-like LRR is a chameleon-like sequence. A duality of two LRR types brings diversity.

Publisher

Bentham Science Publishers Ltd.

Subject

Biochemistry,General Medicine,Structural Biology

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