Histone deacetylases (HDACs) have found intense interest as drug targets for a variety of diseases, but there is disagreement about basic aspects of the inhibition and mechanism of HDACs. QM/MM calculations of HDAC8 including a large QM region provide a model that is consistent with the available crystal structures and structure–activity relationships of different HDAC inhibitors. The calculations support a spontaneous proton transfer from a hydroxamic acid to an active site histidine upon binding to the zinc. The role of the H142/D176 catalytic dyad as the general base of the reaction is elucidated. The reasons for the disagreements between previous proposals are discussed. The results provide detailed insights into the unique mechanism of HDACs, including the role of the two catalytic dyads and function of the potassium near the active site. They also have important implications for the design of novel inhibitors for a number of HDACs such as the class IIa HDACs.

WD40-repeat proteins, as one of the largest protein families, often serve as platforms to assemble functional complexes through the hotspot residues on their domain surfaces, and thus play vital roles in many biological processes. Consequently, it is highly required for researchers who study WD40 proteins and protein–protein interactions to obtain structural information of WD40 domains. Systematic identification of WD40-repeat proteins, including prediction of their secondary structures, tertiary structures and potential hotspot residues responsible for protein–protein interactions, may constitute a valuable resource upon this request. To achieve this goal, we developed a specialized database WDSPdb (http://wu.scbb.pkusz.edu.cn/wdsp/) to provide these details of WD40-repeat proteins based on our recently published method WDSP. The WDSPdb contains 63 211 WD40-repeat proteins identified from 3383 species, including most well-known model organisms. To better serve the community, we implemented a user-friendly interactive web interface to browse, search and download the secondary structures, 3D structure models and potential hotspot residues provided by WDSPdb.

WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar β-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction.

(1R,6R)-2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase (MenH) is an alpha/beta fold enzyme containing a catalytically essential serine-histidine-aspartate triad typical of serine proteases but catalyzes a pyruvate elimination reaction initiated by alpha-proton abstraction in the menaquinone biosynthetic pathway of Escherichia coli. In this study, we identify the active site residues in the synthase through sequence analysis and structural modeling and study their mechanistic roles in MenH catalysis. Steady-state kinetic characterization of site-directed mutants of the active site residues shows that three conserved arginine residues (Arg-90, Arg-124, and Arg-168) likely form ionic salt bridges with three carboxylate groups of the substrate in the Michaelis complex and that the side-chain polar groups of the conserved tyrosine (Tyr-85) and tryptophan (Trp-147) residues likely donate hydrogen bonds to form an "oxyanion hole". In addition, the pH dependence of the MenH kinetic properties reveals a catalytic base with a pK(a) highly dependent on the hydroxyl group of the triad serine residue in the enzymatic reaction. Moreover, proton inventory experiments demonstrate that the SHCHC synthase adopts one-proton catalysis like many serine proteases. These results allow the proposal of a mechanism in which the histidine residue of the MenH triad serves as a general base catalyst to deprotonate the triad seryl hydroxyl group in the alpha-proton abstraction from the substrate. As such, the MenH triad performs a simple and fundamental proton transfer reaction occurring repeatedly in the reactions catalyzed by serine proteases and alpha/beta fold hydrolases, suggesting a common evolutionary origin for all serine-histidine-aspartate triads serving different catalytic functions.

We describe a consanguineous Iraqi family with Leber congenital amaurosis (LCA), Joubert syndrome (JBTS), and polycystic kidney disease. Targeted NGS for excluding mutations in known LCA and JBTS genes, homozygosity mapping and whole-exome sequencing identified a homozygous missense variant, c.317G>C (p.Arg106Pro), in POC1B, a gene essential for ciliogenesis, basal body and centrosome integrity. In silico modeling suggested a requirement of p.Arg106 for formation of the third WD40 repeat and a protein interaction interface. In human and mouse retina, POC1B localized to the basal body and centriole adjacent to the connecting cilium of photoreceptors and in synapses of the outer plexiform layer. Knockdown of Poc1b in zebrafish caused cystic kidneys and retinal degeneration with shortened and reduced photoreceptor connecting cilia, compatible with the human syndromic ciliopathy. A recent study describes homozygosity for p.Arg106ProPOC1B in a family with non-syndromic cone-rod dystrophy. The phenotype associated with homozygous p.Arg106ProPOC1B may thus be highly variable, analogous to homozygous p.Leu710Ser in WDR19 causing either isolated retinitis pigmentosa or Jeune syndrome. Our study indicates that POC1B is required for retinal integrity, and we propose POC1B mutations as a probable cause for JBTS with severe polycystic kidney disease.

The analysis of 36 available crystal structures of WD40 repeat proteins reveals widespread existence of a beta-bulge formed at the beginning of strand a and the end of strand b, termed as WDb–a bulge: among a total of 259 WD40 blades, there are 243 such β-bulges. The R1 positions in these WDb–a bulges have fair distributions of Arg, His, Ile, Leu, Lys, Met, Phe, Trp, Tyr and Val residues. These residues protrude on the top face of the WD40 proteins and can serve as hotspots for protein-protein interactions. An analysis of 29 protein complexes formed by 17 WD proteins reveals that these R1 residues, along with two other residues (R1-2 and D-1), are indeed widely involved in protein-protein interactions. Interestingly, these WDb–a bulges can be easily identified by the 4-amino acid sequences of (V, L, I), R1, R2, (V, L, I), along with some other significant amino acids. Thus, the hotspots of WD40 proteins on the top face can be readily predicted based on the primary sequences of the proteins. The literature-reported mutagenesis studies for Met30, MDV1, Tup11, COP1 and SPA1, which crystal structures are not available, can be readily understood based on the feature-based method. Applying the method, the twelve potential hotspots on the top face of Tup11 from S. japonicas have been identified. Our ITC measurements confirm seven of them, Tyr382, Arg284, Tyr426, Tyr508, Leu559, Lys575 and Ile601, are essential for recognizing Fep1. The ITC measurements further convinced that the feature-based method provides accurate prediction of hotspots on the top face.

The WD40 proteins, often acting as scaffolds to form functional complexes in fundamental cellular processes, are one of the largest families encoded by the eukaryotic genomes. Systematic studies of this family on genome scale are highly required for understanding their detailed functions, but are currently lacking in the animal lineage. Here we present a comprehensive in silico study of the human WD40 family. We have identified 262 non-redundant WD40 proteins, and grouped them into 21 classes according to their domain architectures. Among them, 11 animal-specific domain architectures have been recognized. Sequence alignment indicates the complicated duplication and recombination events in the evolution of this family. Through further phylogenetic analysis, we have revealed that the WD40 family underwent more expansion than the overall average in the evolutionary early stage, and the early emerged WD40 proteins are prone to domain architectures with fundamental cellular roles and more interactions. While most widely and highly expressed human WD40 genes originated early, the tissue-specific ones often have late origin. These results provide a landscape of the human WD40 family concerning their classification, evolution, and expression, serving as a valuable complement to the previous studies in the plant lineage.

New trifluoromethylating reagents are designed based on trans influence and steric effect.