Communication
Structural diversity of leucine-rich repeat proteins1

https://doi.org/10.1006/jmbi.1998.1643Get rights and content

Abstract

The superfamily of leucine-rich repeat proteins can be subdivided into at least six subfamilies, characterised by different lengths and consensus sequences of the repeats. It was proposed that the repeats from different subfamilies retain a similar superhelical fold, but differ in the three-dimensional structures of individual repeats. The sequence-structure relationship of three new subfamilies was examined by molecular modelling. I provide structural models for the repeats of all subfamilies. The models enable me to explain residue conservations within each subfamily. Furthermore, the difference in the packing explains why the repeats from different subfamilies never occur simultaneously in the same protein. Finally, these studies suggest different evolutionary origins for the different subfamilies. The approach used for the prediction of the leucine-rich repeat protein structures can be applied to other proteins containing internal repeats of about 20 to 30 residue in length.

Section snippets

Molecular modelling

The effectiveness of molecular modelling in improving our understanding of the sequence-structure relationship has been demonstrated for LRRs from a typical subfamily Kajava et al 1995, Bhowmick et al 1996, Weber et al 1996. The possibility of a plausible structural prediction is based primarily on two features of LRR proteins. First, as the sequences of LRRs are similar to those of RI repeats, we can assume that the 3D structural arrangement of LRR proteins is superhelical, with one side

The short LRRs occurring in bacteria

The shortest known LRRs are 20 residues long. The analysis shows that some LRR proteins consist entirely of the repeated 20-residue motif without any other domains. The outer membrane protein YopM from Yersinia pestis(Leung & Straley, 1989) has 13 such repeats, while Ipa4 and Ipa7 from Shigella flexneri(Hartman et al., 1990) have eight and six repeats, respectively. All these LRR proteins are extracellular and of Gram-negative bacterial origin. They are essential for bacterial virulence,

Plant-specific LRRs

Sequence analyses shows that some LRRs have a length similar to the typical 24-residue LRR, but their consensus sequences in the variable part differ from the typical LRR consensus (Table 1). The consensus sequence of the repeat differs from the typical 24-residue LRR in a region that corresponds to a half-turn following the conserved “β structure+Asn ladder” region. The consensus sequence of this half-turn region is Lt/sGxIP, compared to LxxLp in the typical LRR subfamily.

Most of these LRR

Cysteine-containing LRRs

In the crystal structure of RI, Asn and Cys alternate with each other at the position immediately following the β strand. Both residues form specific hydrogen bonds with the free peptide groups in the interior of the structure Kobe and Deisenhofer 1993, Kobe and Deisenhofer 1995b. Most LRR proteins have only Asn in this position on the ladder. However, the protein GRR1 from Saccharomyces cerevisiae invariably has Cys in this position (Malvar et al., 1992). The analysis reveals several other

The horseshoe curvature of LRR proteins

The conformation of the variable part of the modelled LRRs range from the polyproline II helix to the α helix. Tightly packed polyproline II helices are closer to each other (8.5 Å) compared with the α helices (10 Å). This suggests that LRR proteins from different subfamilies (at least bacterial and RI-like) may have different curvature of the overall horseshoe structure. The comparison of the energy minimised structure of bacterial LRR protein YopM and the crystal structure of RI shows that

Analysis of the cysteine-rich sequences flanking the LRR arrays

In extracellular proteins, LRR arrays are generally flanked on both N and C-terminal sides by cysteine-rich domains Schneider and Schweiger 1991, Kobe and Deisenhofer 1994. To enlarge the collection of the flanking regions I applied a sequence profile search (Bucher et al., 1996) against a recent release of the GENPEPT database. The analysis results in an identification of four different types of the C-flanking domains. The consensus sequence of the most common type of the C-flanking (CF1)

Conclusion

In conclusion, the sequence analysis allows the subdivision of the large LRR superfamily into at least six subfamilies. LRRs from the different subfamilies never occur concomitantly within one LRR protein. The structural models described here provide an explanation of this mutually exclusive relationship. In the modelled structures, the orientations of the variable non-β-structural parts of LRRs from different subfamilies are different (tilting or shifting relative to the β structure) and

Acknowledgements

I thank Dr B. Kobe for helpful discussion, constructive comments and corrections to the manuscript, and Dr K. Hofmann for valuable suggestions.

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    Edited by F. Cohen

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    Present address: Center for Molecular Modeling, NIH-DCRT, Bldg 12A, Room 2011, Bethesda, MD 20892, USA.

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