The KH Homology (KH) domain is a protein domain that was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. This domain is evolutionarily conserved and consists of approximately 70 amino acids. It is present in a wide variety of nucleic acid-binding proteins and plays a crucial role in RNA recognition and binding .
The KH domain binds RNA and can function in RNA recognition. It is found in multiple copies in several proteins, where they can function cooperatively or independently. For example, in the AU-rich element RNA-binding protein KSRP, which has four KH domains, KH domains 3 and 4 behave as independent binding modules to interact with different regions of the AU-rich RNA targets .
The solution structure of the first KH domain of FMR1 and the C-terminal KH domain of hnRNP K determined by nuclear magnetic resonance (NMR) revealed a beta-alpha-alpha-beta-beta-alpha structure . The KH domain binds to nucleic acids in an extended conformation across one side of the domain. The binding occurs in a cleft formed between alpha helix 1, alpha helix 2, the GXXG loop (which contains a highly conserved sequence motif), and the variable loop .
There are two structurally different types of KH domains identified by Grishin, known as type I and type II . The type I domains are mainly found in eukaryotic proteins, while the type II domains are predominantly found in prokaryotes. While both types share a minimal consensus sequence motif, they have different structural folds. The type I KH domains have a three-stranded beta-sheet where all three strands are anti-parallel. In contrast, the type II domain has two of the three beta strands in a parallel orientation .
Several human proteins contain KH domains, including: