A nested leucine rich repeat (LRR) domain: The precursor of LRRs is a ten or eleven residue motif

Tomoko Mikami,Hiroki Miyashita,Yoshio Kuroki,Norio Matsushima

doi:10.1186/1471-2180-10-235

Tomoko Mikami, Hiroki Miyashita + Show 2 more

Open Access

https://doi.org/10.1186/1471-2180-10-235

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Journal: BMC Microbiology	Publication Date: Jan 1, 2010
Citations: 92	License type: cc-by

Affiliation: Sapporo Medical University

Abstract

BackgroundLeucine rich repeats (LRRs) are present in over 60,000 proteins that have been identified in viruses, bacteria, archae, and eukaryotes. All known structures of repeated LRRs adopt an arc shape. Most LRRs are 20-30 residues long. All LRRs contain LxxLxLxxNxL, in which "L" is Leu, Ile, Val, or Phe and "N" is Asn, Thr, Ser, or Cys and "x" is any amino acid. Seven classes of LRRs have been identified. However, other LRR classes remains to be characterized. The evolution of LRRs is not well understood.ResultsHere we describe a novel LRR domain, or nested repeat observed in 134 proteins from 54 bacterial species. This novel LRR domain has 21 residues with the consensus sequence of LxxLxLxxNxLxxLDLxx(N/L/Q/x)xx or LxxLxCxxNxLxxLDLxx(N/L/x)xx. This LRR domain is characterized by a nested periodicity; it consists of alternating 10- and 11- residues units of LxxLxLxxNx(x/-). We call it "IRREKO" LRR, since the Japanese word for "nested" is "IRREKO". The first unit of the "IRREKO" LRR domain is frequently occupied by an "SDS22-like" LRR with the consensus of LxxLxLxxNxLxxLxxLxxLxx or a "Bacterial" LRR with the consensus of LxxLxLxxNxLxxLPxLPxx. In some proteins an "SDS22-like" LRR intervenes between "IRREKO" LRRs.ConclusionProteins having "IRREKO" LRR domain are almost exclusively found in bacteria. It is suggested that IRREKO@LRR evolved from a common ancestor with "SDS22-like" and "Bacterial" classes and that the ancestor of IRREKO@LRR is 10 or 11 residues of LxxLxLxxNx(x/-). The "IRREKO" LRR is predicted to adopt an arc shape with smaller curvature in which β-strands are formed on both concave and convex surfaces.

Highlights

Leucine rich repeats (LRRs) are present in over 60,000 proteins that have been identified in viruses, bacteria, archae, and eukaryotes
Proteins having IRREKO@LRRs We identified a total of 134 IRREKO@LRR proteins from 54 bacterial species including Escherichia, Shigella, Vibrio, Shewanella, Photobacterium, Bifidobacterium, Porphyromonas, Treponema, Listeria, Alistipes, Bacteroides, Clostridium, Cytophaga, and Flavobacterium (Additional file 1, Table 1)
IRREKO@LRR proteins from Vibrio, Shewanella, and Photobacterium have an LRRNT with the pattern of Cx16C (Additional file 1, Table 1)

Summary

Introduction

Leucine rich repeats (LRRs) are present in over 60,000 proteins that have been identified in viruses, bacteria, archae, and eukaryotes. All LRRs contain LxxLxLxxNxL, in which “L” is Leu, Ile, Val, or Phe and “N” is Asn, Thr, Ser, or Cys and “x” is any amino acid. LRR (leucine rich repeat) domains are present in over 60, 000 proteins listed in PFAM, PRINTS, SMART, InterPro and PANTHER databases [1]. LRR-containing proteins have been identified in viruses, bacteria, archae, and eukaryotes. The HCS part consists of an eleven residue stretch, LxxLxLxxNxL, or a twelve residue stretch, LxxLxLxxCxxL, in which “L” is Leu, Ile, Val, or Phe, “N” is Asn, Thr, Ser, or Cys, and “C” is Cys, Ser or Asn. Three residues at positions 3 to 5 in the highly conserved segments form a short “Typical” LRRs are the most abundant LRR class. Bold uppercase letters indicate more than 70% occurrence of a given residue in a certain position; normal letters indicate 40-70% occurrence and lowercase letters indicate 30-40%

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