title: A nested leucine rich repeat (LRR) domain: the precursor of LRRs is a ten or eleven residue motif.
abstract: BACKGROUND
  Leucine 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.
  
  
  RESULTS
  Here 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.
  
  
  CONCLUSIONS
  Proteins 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.
authors.affiliation: Sapporo Medical University Center for Medical Education, Sapporo, Hokkaido 060-8556, Japan. matusima@sapmed.ac.jp
authors.forename: Norio
authors.initials: N
authors.lastname: Matsushima
authors.forename: Hiroki
authors.initials: H
authors.lastname: Miyashita
authors.forename: Tomoko
authors.initials: T
authors.lastname: Mikami
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Kuroki
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001419:Bacteria / Q000737:chemistry / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D016384:Consensus Sequence; D019143:Evolution, Molecular; D007930:Leucine / Q000737:chemistry* / Q000235:genetics; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D020449:Repetitive Sequences, Amino Acid
chemical_list: D001426:Bacterial Proteins; D007930:Leucine
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