Vilela-Alves, G, Manuel RR, Pedrosa N, Cardoso Pereira IA, Romão MJ, Mota C.
2024.
{Structural and biochemical characterization of the M405S variant of ıt Desulfovibrio vulgaris} formate dehydrogenase}, May. Acta Crystallographica Section F. 80:98–106., Number 5
AbstractMolybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO${\sb 2}$ to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of ıt Desulfovibrio vulgaris} formate dehydrogenase AB (ıt Dv}FdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine S${\sp {$δ$}}$ interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO${\sb 2}$ reduction, together with an increased sensitivity to oxygen inactivation.
Ribeiro, DO, Bonnardel F, Palma AS, Carvalho ALM, Perez S.
2024.
CBMcarb-DB: interface of the three-dimensional landscape of carbohydrate-binding modules, 2024/06/26. Carbohydrate Chemistry: Chemical and Biological Approaches Volume 46. 46(
Pilar Rauter, Amélia, Queneau, Yves, Palma, Angelina Sá, Eds.).: Royal Society of Chemistry
AbstractCarbohydrate-binding-modules (CBMs) are discrete auxiliary protein modules with a non-catalytic carbohydrate-binding function and that exhibit a great diversity of binding specificities. CBMcarb-DB is a curated database that classifies the three-dimensional structures of CBM–carbohydrate complexes determined by single-crystal X-ray diffraction methods and solution NMR spectroscopy. We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. Special attention was devoted to describing the bound glycans using simple graphical representation and numerical format for cross-referencing to other glycosciences and functional data databases. CBMcarb-DB provides detailed information on CBMs and their bound oligosaccharides and features their interactions using several open-access applications. We also describe how the curated information provided by CBMcarb-DB can be integrated with AI algorithms of 3D structure prediction, facilitating structure–function studies. Also in this chapter, we discuss the exciting convergence of CBMcarb-DB with the glycan array repository, which serves as a valuable resource for investigating the specific binding interactions between glycans and various biomolecular targets. The interaction of the two fields represents a significant milestone in glycosciences. CBMcarb-DB is freely available at https://cbmdb.glycopedia.eu/ and https://cbmcarb.webhost.fct.unl.pt.