Biology subjects

Urdiain-Arraiza, J.

Publications and source records attributed to Urdiain-Arraiza, J..

3 recordsLinked to original sources

bioRxiv2026

Dimerization of the S. cerevisiae Spo11 core complex

Spo11 initiates meiotic recombination by introducing programmed DNA double-strand breaks. DNA cleavage occurs via a topoisomerase-like mechanism involving hybrid active sites formed at the dimer interface. However, in contrast to its topoisomerase relative (Topo VI), Spo11 does not form a stable dimer, likely to prevent uncontrolled DNA cleavage. Here, we investigated the dimerization of S. cerevisiae Spo11 in complex with its partners Ski8, Rec102, and Rec104. We show that the Spo11 complex dimerizes transiently on DNA, forming unstable dimeric complexes with duplex and branched DNA substrates. Guided by AlphaFold modeling of a pre-cleavage complex, we identified mutations that reduce dimerization. Surprisingly, DSB formation is resilient to mutagenesis of the Spo11 dimer interface, implying that additional factors promote dimerization in vivo. Finally, we found that Rec102 exerts a key DNA-binding function, essential for catalysis, and show that it also participates in dimerization through trans contacts with Ski8. Our work provides new insights into the mechanism of Spo11 dimerization and the role of its partners in initiating meiotic recombination.

molecular biology↗

bioRxiv2025

Structures of two LarA-like nickel-pincer nucleotide cofactor-utilizing enzymes with a single catalytic histidine residue

The nickel pincer nucleotide (NPN) cofactor catalyzes the racemization/epimerization of -hydroxy acids in enzymes of the LarA family. The established proton-coupled hydride transfer mechanism requires two catalytic histidine residues that alternately act as general acids and general bases. Notably, however, a fraction of LarA homologs (LarAHs) lack one of the active site histidine residues, replacing it with an asparaginyl side chain that cannot participate in acid/base catalysis. Here, we investigated two such LarAHs and solved their cryo-electron microscopic structures with and without loaded NPN cofactor, respectively. The structures revealed a consistent octameric assembly that is unprecedented in the LarA family and unveiled a new set of active site residues that likely recognize and process substrates differently from those of the well-studied LarAHs. Genomic context analysis suggested their potential involvement in carbohydrate metabolism. Together, these findings lay the groundwork for expanding the breadth of reactions and the range of mechanisms of LarA enzymes.

biochemistry↗

bioRxiv2024

Structural Basis for Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum

The LarA family consists of diverse racemases/epimerases that interconvert the diastereomers of a variety of -hydroxyacids by using a nickel-pincer nucleotide (NPN) cofactor. The hidden redox reaction catalyzed by the NPN cofactor makes LarA enzymes attractive engineering targets for applications. However, how a LarA enzyme binds its natural substrate and recognizes different -hydroxyacids has not been elucidated. Here, we report three high-resolution structures of the enzyme-substrate complexes of a broad-spectrum LarA enzyme from Isosphaera pallida (LarAIp). The substrate binding mode reveals an optimal orientation and distance between the hydride donor and acceptor, strongly supporting the proposed proton-coupled hydride transfer mechanism. The experimentally solved structures, together with the structural models of other LarA enzymes, allow us to identify the residues/structural elements critically involved in the interactions with different -hydroxyacid substrates. Collectively, this work provides a critical structural basis for catalysis and substrate recognition of the diverse enzymes in the LarA family, thus building a foundation for enzyme engineering.

biochemistry↗