Protein target highlights in CASP15: Analysis of models by structure providers

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.

Structural studies reveal unique features of nsp16 from SARS‐CoV‐2, a protein essential for immune system evasion and a possible drug target

RNA viruses have several mechanisms to modify the viral RNA genome to protect from host immune surveillance. SARS‐CoV‐2, the etiological agent of COVID‐19, and other coronaviruses encode capping proteins in its genome that modify the 5’ untranslated region of the viral genome and mRNA. Capping viral RNAs promotes translation, prevents degradation, and reduces the activation of host immune responses. This process is initiated by the viral proteins nsp13 and nsp12, which cleave the 5’ phosphate group and transfer a GMP from GTP to the 5′ end of the nascent (+)ssRNA. The nsp14‐nsp10 complex then catalyzes the transfer of a methyl group from S‐adenosylmethionine (SAM) to the N7 position of the GMP cap, generating Cap‐0. Finally, the nsp16‐nsp10 complex utilizes SAM to catalyze the 2′‐O‐methylation of the first ribonucleotide, generating Cap‐1. Several structures of the nsp16‐nsp10 complex have been solved previously for SARS‐CoV, MERS and SARS‐CoV‐2 with SAM, Cap‐0 and Cap‐0‐RNA bound to the complex as well as the products of the reactions. Recently, we determined the first structure of nsp16‐nsp10 with Cap‐0‐RNA and Cap‐1 RNA, revealing that Mn2+ coordinates the first four nucleotides of the bound RNA to orient the 2’‐OH of the ribose of the first nucleotide toward the methyl group of SAM for catalysis. Herein, we also show the first apo‐crystal structure of nsp16 determined in which neither SAM nor RNA substrates bound. This new structure and comparison to structures with substraces and products bound, will reveal critical movements of the enzyme for binding substates. This study shows an important set of structures of the viral 2’‐O‐methyltransferases revealing unique features of this complex that could be used for molecular dynamics studies and designing coronavirus‐specific inhibitors.

Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment

Galactarate dehydratase (GarD) is the first enzyme in the galactarate/glucarate pathway and catalyzes the dehydration of galactarate to 3-keto-5-dehydroxygalactarate. This protein is known to increase colonization fitness of intestinal pathogens in antibiotic-treated mice and to promote bacterial survival during stress. The galactarate/glucarate pathway is widespread in bacteria, but not in humans, and thus could be a target to develop new inhibitors for use in combination therapy to combat antibiotic resistance. The structure of almost all the enzymes of the galactarate/glucarate pathway were solved previously, except for GarD, for which only the structure of the N-terminal domain was determined previously. Herein, we report the first crystal structure of full-length GarD solved using a seleno-methoionine derivative revealing a new protein fold. The protein consists of three domains, each presenting a novel twist as compared to their distant homologs. GarD in the crystal structure forms dimers and each monomer consists of three domains. The N-terminal domain is comprised of a β-clip fold, connected to the second domain by a long unstructured linker. The second domain serves as a dimerization interface between two monomers. The C-terminal domain forms an unusual variant of a Rossmann fold with a crossover and is built around a seven-stranded parallel β-sheet supported by nine α-helices. A metal binding site in the C-terminal domain is occupied by Ca2+ . The activity of GarD was corroborated by the production of 5-keto-4-deoxy-D-glucarate under reducing conditions and in the presence of iron. Thus, GarD is an unusual enolase with a novel protein fold never previously seen in this class of enzymes.