Unique Super-Secondary Structures for Novel Leucine-Rich Repeats in Many Proteins from the Bacterial PVC Superphylum

The sequence, structure, function relationship in proteins is still significant and meaningful to understanding structural principles Tandem leucine-rich repeats (LRRs) have been well classified into eleven canonical LRR types. We identified novel LRR motifs having a dual characteristic of two canonical types in over 3,600 proteins, mainly from the bacterial PVC superphylum, by using sequence similarity searches. We studied their structures using AlphaFold and their biological functions by using protein domain searches. The novel LRR motifs are classified into three groups. The first and second groups are characterized by the consensuses of LxxLxLxx(C/T)xzI TDxxLxx(L/F)xx(L/C)xx, LxxLxLxxCxxI TDxxLxxLxxLP in which “z” shows a deletion. A new canonical type with the consensus sequence LxxLxLxx(T/N/C)xzV xxLxPLxxMx was identified as the third group. AlphaFold predicts that all of the LRR domains form a solenoid structure by the parallel stacking of β-strands. The LRR domains are mostly characterized by two unique super-secondary structures (SSSs) of β-strand – α-helix adjoining 3(10)-helix – β-strand motif and β-strand – 3(10)-helix – β-strand motif and a well-known SSS of β-strand – α-helix – β-strand motif. Many LRR proteins containing a kinase domain or an F-box domain might be involved in bacterial immunity or ubiquitination. We suggest that the former two SSSs are a fundamental motif in protein structure.