A nested leucine rich repeat (LRR) domain: the precursor of LRRs is a ten or eleven residue motif.
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.
Matsushima
Norio
N
Sapporo Medical University Center for Medical Education, Sapporo, Hokkaido 060-8556, Japan. matusima@sapmed.ac.jp
Miyashita
Hiroki
H
Mikami
Tomoko
T
Kuroki
Yoshio
Y
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
D001426:Bacterial Proteins; D007930:Leucine
J Appl Genet. 2002;43(4):403-14
12441626
Cell. 2007 Sep 7;130(5):906-17
17803912
Plant Cell. 2005 Mar;17(3):1000-15
15722474
Annu Rev Phytopathol. 2001;39:285-312
11701867
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W202-9
18483082
Curr Opin Plant Biol. 2000 Aug;3(4):278-84
10873844
Genome Res. 1998 Nov;8(11):1113-30
9847076
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W72-6
15980571
Plant Mol Biol. 2000 Jan;42(1):195-204
10688137
Curr Opin Plant Biol. 1998 Aug;1(4):294-8
10066604
J Mol Biol. 1998 Apr 3;277(3):519-27
9533877
Curr Opin Plant Biol. 2000 Aug;3(4):285-90
10873848
Curr Opin Struct Biol. 2001 Dec;11(6):725-32
11751054
Mol Plant Microbe Interact. 2006 Mar;19(3):288-303
16570659
Plant Physiol. 2005 Jun;138(2):611-23
15955925
Cell Mol Life Sci. 2008 Aug;65(15):2307-33
18408889
BMC Genomics. 2007 May 21;8:124
17517123
Plant Physiol. 2008 Jun;147(2):503-17
18434605
Prog Biophys Mol Biol. 2001 Oct;77(2):111-75
11747907
Trends Genet. 2004 Mar;20(3):116-22
15049302
Methods Mol Biol. 2007;396:43-58
18025685
BMC Evol Biol. 2007 Nov 16;7:231
18021397
Cell. 2007 Sep 21;130(6):1071-82
17889651
Mol Biochem Parasitol. 2002 Nov-Dec;125(1-2):195-9
12467987
Proteins. 2004 Feb 15;54(3):394-403
14747988
Biochim Biophys Acta. 2009 Oct;1790(10):1217-37
19580846
J Mol Biol. 2000 May 5;298(3):521-37
10772867
PLoS One. 2008 Feb 27;3(2):e1694
18301771
J Mol Biol. 2004 Jul 16;340(4):783-95
15223320
Trends Biochem Sci. 2000 Oct;25(10):509-15
11050437
Proteins. 2000 Feb 1;38(2):210-25
10656267
Int Rev Cytol. 2004;234:1-46
15066372
J Mol Biol. 1994 Sep 23;242(3):244-51
8089845
J Struct Biol. 1998;122(1-2):236-46
9724625
Trends Biochem Sci. 1994 Oct;19(10):415-21
7817399
Cell Mol Life Sci. 2005 Dec;62(23):2771-91
16231091