Characteristics of the Kelch domain containing (KLHDC) subfamily and relationships with diseases

Abstract

The Kelch protein superfamily is an evolutionary conserved family containing 63 alternate protein coding members. The superfamily is split into three subfamilies: Kelch like (KLHL), Kelch-repeat and bric-a-bracs (BTB) domain containing (KBTBD) and Kelch domain containing protein (KLHDC). The KLHDC subfamily is one of the smallest within the Kelch superfamily, containing 10 primary members. There is little known about the structures and functions of the subfamily; however, they are thought to be involved in several cellular and molecular processes. Recently, there have been significant structural and biochemical advances for KLHDC2, which has aided our understanding of other KLHDC family members. Furthermore, small molecules directly targeting KLHDC2 have been identified, which act as tools for targeted protein degradation. This review utilises this information, in conjunction with a thorough exploration of the structural aspects and potential biological functions to summarise the relationship between KLHDCs and human disease.

Keywords: KLHDC; Kelch family; protein degradation; protein function.

Fig. 1

Kelch protein superfamily. There are three subfamilies – Kelch like (KLHL), Kelch‐repeat and bric‐a‐bracs domain containing (KBTBD) and Kelch domain containing protein (KLHDC). Initial phylogenetic analysis suggested 12 members of the KLHDC subfamily (left); however, recent evidence has suggested that there are only 10 subfamily members [95].

Fig. 2

Schematic of structural differences between each KLHDC sub‐family member. In order top to bottom: KLHDC1, KLHDC2, KLHDC3, KLHDC4, KLHDC7A, KLHDC7B, KLHDC8A, KLHDC8B, KLHDC9, KLHDC10. Pink box: single Kelch repeat; green circle/oval: unknown complex; orange hexagon: predicted BACK complex; blue bubble: disordered region; purple inverted hexagon: predicted NHL repeat complex. Analysis was completed using alphafold structures; these structures, along with an X‐ray crystal structure of KLHDC2 (PDB: 8EBN, with other complexes removed), were used to analyse and compare the structural domains of the different family members.

Fig. 3

Alignment of Kelch β‐propeller of each of the KLHDC subfamily members. Protein sequences of human KLHDC subfamily members obtained from UniProt (codes within figure). Dots indicate every tenth amino acids of the protein sequence. Magenta bar: gly‐gly doublet; cyan bar: aromatic residue Tryptophan. White letters on black background: identical amino acids; bold letters in green box: highly similar amino acids according to physico‐chemical properties; standard letters: different amino acids. Alignment was performed using clustal omega [96].

Fig. 4

Predicted structures of KLHDC sub‐family. (A) Predicted crystal structure of KLHDC1 (AF_Q8N7A1‐F1), (B) experimental crystal structure of KLHDC2 from Scott et al. [22] (PDB: 8EBN), (C) predicted crystal structure of KLHDC3 (AF‐Q9BQ90‐F1), (D) predicted crystal structure of KLHDC4 (AF‐Q8TBB5‐F1), (E) predicted crystal structure of KLHDC7A (AF‐Q5VTJ3‐F1), (F) predicted crystal structure of KLHDC7B (AF_Q96G42‐F1), (G) predicted crystal structure of KLHDC8A (AF‐Q8IYD2‐F1), (H) predicted crystal structure of KLHDC8B (AF_Q8IXV7‐F1), (I) predicted crystal structure of KLHDC9 (AF‐Q8NEP7‐F1) and (J) predicted crystal structure of KLHDC10 (AF‐Q6PID8‐F1). All structures obtained from alphafold2 [13] and visualised in pymol (the pymol molecular graphics system, version 3.0 schrödinger, llc.).

Fig. 5

Schematic of KLHDC role in ubiquitination. Left panel: Simplified schematic of the cascade process for ubiquitination to occur. E1 activates Ub through a thioester bond in an ATP‐dependent process. Then, the activated Ub is ‘transferred’ to an E2 enzyme's active‐site cysteine. Finally, an E3 ligase recognises the E2 complex and transfers Ub from E2 to the target substrate. Based on how Ub binds to the substrate, ubiquitination can be mono‐, multi‐, or poly‐ubiquitination. Right panel: Schematic of three E3 CRL complexes specific to this review; Cul2, Cul3 and Cul5 recruit specific adaptor proteins (Elongin B/C for Cul2 and Cul5, BTB protein for Cul3) and receptor proteins (VHL‐box for Cul2, SOCS for Cul5) to form CRL E3 ubiquitin ligases with the RING protein (Rbx1/2). These ligases transfer ubiquitin from Rbx1/2‐bound E2 to substrate proteins. Figures adapted from [45].