Bufton, J. C. | Search bioRxiv

bioRxiv2024

A BTB extension and ion-binding domain contribute to the pentameric structure and TFAP2A binding of KCTD1

KCTD family proteins typically assemble into Cullin-RING E3 ligases. KCTD1 is an atypical member that functions instead as a transcriptional repressor. Mutations in KCTD1 cause developmental abnormalities and kidney fibrosis in scalp-ear-nipple syndrome. Here, we present unexpected mechanistic insights from the structure of full-length KCTD1. Disease-causing mutation P20S maps to an unrecognized extension of the BTB domain that contributes both to its pentameric structure and TFAP2A binding. The C-terminal domain (CTD) shares its fold and pentameric assembly with the protein GFRP despite lacking discernible sequence similarity. Most surprisingly, the KCTD1 CTD establishes a central channel occupied by alternating sodium and iodide ions that restrict TFAP2A dissociation. The elucidation of the structure redefines the KCTD family BTB domain fold and identifies an unexpected ion pore for future study of KCTD1s function in the ectoderm, neural crest and kidney.

molecular biology↗

bioRxiv2022

Molecular basis of neurodevelopmental disorder-causing mutation in nonsense-mediated mRNA decay factor UPF3B

UPF3B is a key nonsense-mediated mRNA decay (NMD) factor required for surveillance of mRNA and regulation of eukaryotic gene expression. Mutations in UPF3B cause intellectual disability. The underlying molecular mechanisms remain unexplored as the mutations lie in an uncharacterized region of UPF3B. Here, we show that UPF3B shares structural and functional homology to the Drosophila Behavior/Human Splicing protein family comprising an RNA-recognition motif-like domain (RRM-L), a NONA/paraspeckle-like domain (NOPS-L), and extended -helical domains essential for ribosome- and RNA-binding and RNA-induced oligomerization. A co-crystal structure of UPF3B with the third middle domain of eukaryotic initiation factor 4G (MIF4GIII) of UPF2 reveals an unexpectedly intimate binding interface. UPF3Bs disease-causing mutation Y160D located in the NOPS-L domain reduces the UPF2 binding affinity ~40-fold compared to wildtype UPF3B. UPF3Bs paralogue UPF3A, an NMD antagonist which is upregulated in patients with the UPF3B-Y160D mutation, binds UPF2 with ~10-fold higher affinity than UPF3B, leading to impaired NMD activity and upregulation of mRNAs involved in neurodevelopment.

biochemistry↗