Structure and function of KH domains

Abstract

The hnRNP K homology (KH) domain was first identified in the protein human heterogeneous nuclear ribonucleoprotein K (hnRNP K) 14 years ago. Since then, KH domains have been identified as nucleic acid recognition motifs in proteins that perform a wide range of cellular functions. KH domains bind RNA or ssDNA, and are found in proteins associated with transcriptional and translational regulation, along with other cellular processes. Several diseases, e.g. fragile X mental retardation syndrome and paraneoplastic disease, are associated with the loss of function of a particular KH domain. Here we discuss the progress made towards understanding both general and specific features of the molecular recognition of nucleic acids by KH domains. The typical binding surface of KH domains is a cleft that is versatile but that can typically accommodate only four unpaired bases. Van der Waals forces and hydrophobic interactions and, to a lesser extent, electrostatic interactions, contribute to the nucleic acid binding affinity. ‘Augmented’ KH domains or multiple copies of KH domains within a protein are two strategies that are used to achieve greater affinity and specificity of nucleic acid binding. Isolated KH domains have been seen to crystallize as monomers, dimers and tetramers, but no published data support the formation of noncovalent higher‐order oligomers by KH domains in solution. Much attention has been given in the literature to a conserved hydrophobic residue (typically Ile or Leu) that is present in most KH domains. The interest derives from the observation that an individual with this Ile mutated to Asn, in the KH2 domain of fragile X mental retardation protein, exhibits a particularly severe form of the syndrome. The structural effects of this mutation in the fragile X mental retardation protein KH2 domain have recently been reported. We discuss the use of analogous point mutations at this position in other KH domains to dissect both structure and function.

Drosophila Pur-α binds to trinucleotide-repeat containing cellular RNAs and translocates to the early oocyte

“…Assembly of multiple RNA binding sites is a common strategy among RNA transport factors that likely increases affinity, specificity or halflife of the mRNP complex, i.e., the chance for the cargo to remain bound throughout the entire transport time. 26 The binding affinities we determined in vitro are significantly higher than previously thought but still in a moderate range (150 nM and higher). Considering the solution structure model calculated from SAXS-data, a 12-mer RNA binding substrate may be too short to make contacts with more than one pur-domain.…”

The Extra-Membranous Domains of the Competence Protein HofQ Show DNA Binding, Flexibility and a Shared Fold with Type I KH Domains

“…The second domain of emHofQ displays high structural similarity to the nucleotide-binding KH domain of Nova-1 ( Figure 4B). KH domains contain a conserved GxxG motif involved in nucleotide binding 49,50 and a GGSG motif is found in similar location structurally in emHofQ. Furthermore, the second domain of emHofQ is related to domain 1 in both in structure and sequence ( Figure 3B, C).…”

“…All typical KH domains contain a conserved GxxG motif, 50 which is involved in nucleotide binding. 49 A GxxG motif is also found in emHofQ, with residues 149-152 having the sequence GGSG, and the two motifs in emHofQ and the KH domain are situated in close proximity structurally ( Figure 4B inset).…”

“…These domains are often involved in DNA or RNA binding, 48,49 which is of particular interest given the proposed role of emHofQ in DNA uptake. The second domain of emHofQ can be superimposed onto the KH domain of the neuronal splicing factor Nova-1 RNA binding protein (PDB ID: 2ANN) (unpublished) with a Z score of 6.7 and rmsd of 2.2 Å over 61 aligned residues ( Figure 3B).…”

Analysis of protein–RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry

“…In the case of UV-induced protein-RNA cross-linking, MS has been applied to identify the cross-linked proteins by standard quantitative MS-based proteomic approaches [11][12][13]. Subsequent database-searching has led to the identification of conserved structural motifs in these proteins [2], such as RNA-recognition motifs (RRMs) [14], K homology (KH) domains [15], zinc-finger domains [16], tudor domains [17], double-stranded RNA binding domains (dsRBDs) [18], G-patch domains [19], Sm motifs [20] etc. However, such proteomic approaches yield little or no information about (i) whether the protein cross-links to the RNA through its canonical RBD or through other domains within the protein; (ii) which RBD is involved in interaction with RNA when the proteins contains several potential RBDs; (iii) how proteins that do not harbor any known RBD (as identified by sequence) interact with RNA.…”