xtal

Vilela-Alves, G, Manuel RR, Martins G, Carpentier P, Raczyńska A, Szaleniec M, Pereira ICA, Romão MJ, Mota C.  2026.  Structural Insights Into CO2 Transport Pathways in a W-Formate Dehydrogenase: Structural Basis for CO2 Reduction, 2026. Angewandte Chemie International EditionAngewandte Chemie International Edition. 65(16):e26133.: John Wiley & Sons, Ltd AbstractWebsite

ABSTRACT Mo/W-dependent formate dehydrogenases (Fdhs) catalyze the reversible reduction of CO2 to formate and are key biocatalysts with high potential for CO2 capture/conversion technologies. Although previous studies have suggested the presence of two substrate-access tunnels in Fdhs, experimental evidence for CO2-specific pathways has been lacking. Here, we present an integrated study of Nitratidesulfovibrio vulgaris FdhAB combining crystallography, molecular dynamics simulations, mutagenesis, and kinetic assays. NvFdhAB crystals pressurized with Kr, O2, and CO2 were used to map gas diffusion routes and uncovered a substrate-retention site consistently occupied by small molecules in multiple crystal structures. Our results indicate that both substrates mostly use the main tunnel to reach this retention site, but H2O and CO2 can also enter through a novel side branch before following a shared route to the buried W active site. The retention site, located at the junction of both tunnels, plays a synergistic role in enhancing CO2 reduction by increasing substrate concentration near the catalytic center, thereby improving catalytic efficiency. Notably, variants affecting this site showed a selective effect for CO2 reduction, with no impact on formate oxidation. These findings provide experimental evidence of a CO2-specific pathway and identify structural determinants underpinning efficient CO2 reduction in this enzyme family.

Ana Luísa Carvalho and Guilherme Vilela Alves represented XTAL at the Instruct-PT Day.

The Instruct-PT Day took place at ITQB-NOVA on February 13, bringing together researchers to share advances in structural biology and related fields.

Monge, N, Pinto LFV, Ferreira E, Almeida PL, Figueirinhas JL, Carvalho AL, Sebastião PJ, Godinho MH.  2026.  Hierarchical Twist: Chirality Across Scales in Cellulose Cholesterics, 2026. Advanced Optical MaterialsAdvanced Optical Materials. 14(4):e02728.: John Wiley & Sons, Ltd AbstractWebsite

Abstract One of the unresolved aspects of cellulose-based liquid crystalline phases is their chirality. Although cellulose is intrinsically chiral, both left-handed (LH) and right-handed (RH) chiral nematic phases are reported in cellulose derivatives under different conditions. The origin of these discrepancies?and whether LH and RH twisted structures coexist within a single material?has remained unclear. Here, the first direct evidence of hierarchical LH and RH twisted structures coexisting in a solvent-free, thermotropic cellulose derivative at room temperature is provided. Free-standing cholesteric films exhibit distinct LH and RH twisted domains, whose pitches respond oppositely to uniaxial mechanical strain: the LH pitch increases, while the RH pitch decreases with increasing strain. This contrasting response results from the coexistence of intertwined LH and RH twisted structures, whose optical axes are oriented differently relative to the strain direction. Notably, after stretching beyond their elastic limit, the films spontaneously recover their original shape within minutes. During this recovery, circular dichroism (CD) measurements reveal an increase in RH pitch and a decrease in LH pitch, evidencing reversible, strain-responsive behavior. Multiscale structural characterization confirms the hierarchical chiral organization and its mechanoresponsive nature, providing new insights into the origin of chirality in cellulose-based liquid crystalline materials.

Romao, MJ, Vilela-Alves G, Mota C.  2025.  Mammalian Aldehyde Oxidase, 2025/11/10. Iron‐Sulfur Clusters. :135-158. Abstract

Summary Mammalian aldehyde oxidases (AOXs) are complex enzymes dependent on a molybdopterin-active site (Moco), two [2Fe?2S] spectroscopically distinct centers, and one flavin adenine dinucleotide (FAD) cofactor. AOXs belong to the xanthine oxidase (XO) family of mononuclear molybdenum enzymes. AOXs and XO share a high degree of structural similarity forming homodimers that encompass in each subunit a chain of redox centers involved in the transfer of reducing equivalents from substrate oxidation (Moco ? [2Fe?2S] I ? [2Fe?2S] II? FAD) to molecular oxygen. However, AOXs and XO differ in substrate specificity and, while XO has a clear role in the last steps of purine catabolism, AOXs are very promiscuous enzymes. They catalyze a wide diversity of reactions, accept diverse substrates, and play an important role in drug and xenobiotic metabolism. Despite numerous studies, the physiological substrates of AOX and its physiological relevance are still unclear.

Oliveira, AR, Vilela-Alves G, Mota C, Léger C, Fourmond V, Biaso F, Guigliarelli B, Romão MJ, Pereira ICA.  2025.  The Role of Selenocysteine in Catalysis and Oxygen Tolerance of a W-Dependent Formate Dehydrogenase, 2025. ACS CatalysisACS Catalysis. 15(15):12627-12639.: American Chemical Society AbstractWebsite

Metal-dependent formate dehydrogenases (FDHs) catalyze, under mild conditions, the reversible reduction of CO2 to formate, a versatile C1 feedstock that can contribute to a carbon-neutral economy. Metal-dependent FDHs are the most widespread selenoproteins found in bacteria, and around 44% of them include selenocysteine (Sec) as a ligand to the Mo/W active site. In the sulfate-reducer Nitratidesulfovibrio vulgaris Hildenborough, the main FDH responsible for CO2 reduction is the W/Sec-dependent FdhAB, which is among the most active CO2 reductases reported so far. In contrast to most metal-dependent FDHs, this enzyme is relatively O2-tolerant and can be purified aerobically. In this work, we evaluated the role of Sec in the catalytic and stability properties of the W/Sec-FdhAB. For that, a Sec-to-Cys variant (U192C) was created, its catalytic and spectroscopic properties were characterized, and its crystal structure was determined. Sec substitution by Cys strongly affects activity, decreases the KM for formate, and increases susceptibility to O2. While Sec-to-Cys replacement induces only weak changes of the WV EPR signals, using 77Se-labeled enzyme, we could show that Sec undoubtedly coordinates the W metal in the WV redox state. The crystal structure of U192C confirmed previous findings on the redox switch mechanism of activation and protection of FdhAB, while revealing a putative catalytic intermediate of FdhAB with Arg441 orienting a CO2 substrate analog (probably SO2) in the active site. Overall, the results indicate that Sec plays a critical role in the high activity displayed by W/Sec-FdhAB, and that it may also be involved in or modulate the proton transfer to and from the active site.Metal-dependent formate dehydrogenases (FDHs) catalyze, under mild conditions, the reversible reduction of CO2 to formate, a versatile C1 feedstock that can contribute to a carbon-neutral economy. Metal-dependent FDHs are the most widespread selenoproteins found in bacteria, and around 44% of them include selenocysteine (Sec) as a ligand to the Mo/W active site. In the sulfate-reducer Nitratidesulfovibrio vulgaris Hildenborough, the main FDH responsible for CO2 reduction is the W/Sec-dependent FdhAB, which is among the most active CO2 reductases reported so far. In contrast to most metal-dependent FDHs, this enzyme is relatively O2-tolerant and can be purified aerobically. In this work, we evaluated the role of Sec in the catalytic and stability properties of the W/Sec-FdhAB. For that, a Sec-to-Cys variant (U192C) was created, its catalytic and spectroscopic properties were characterized, and its crystal structure was determined. Sec substitution by Cys strongly affects activity, decreases the KM for formate, and increases susceptibility to O2. While Sec-to-Cys replacement induces only weak changes of the WV EPR signals, using 77Se-labeled enzyme, we could show that Sec undoubtedly coordinates the W metal in the WV redox state. The crystal structure of U192C confirmed previous findings on the redox switch mechanism of activation and protection of FdhAB, while revealing a putative catalytic intermediate of FdhAB with Arg441 orienting a CO2 substrate analog (probably SO2) in the active site. Overall, the results indicate that Sec plays a critical role in the high activity displayed by W/Sec-FdhAB, and that it may also be involved in or modulate the proton transfer to and from the active site.

Congratulations, Doctor Filipa Engrola!

On Friday, November 14th, Filipa Engrola successfully defended her PhD in Biochemistry, with a thesis entitled: “Understanding Molybdenum Enzymes through Structural and Biophysical Techniques: Pathways to Biotechnological innovation”, supervised by Teresa Santos Silva and Aldino Viegas.

Cristiano Mota has just started a new position as Assistant Professor!

Wishing you every success in your new position at NOVA FCT, Cristiano. Your dedication and excellent work are truly appreciated, and you can always rely on the support of your XTAL colleagues!

Congratulations, Doctor João Paquete Ferreira!

On Wednesday, July 16th, João Paquete Ferreira successfully defended his PhD in Biochemistry, with a thesis entitled: “From proteins to Bacteria: a multidisciplinary approach for the rational development of new antibiofilm and antibacterial agents” and supervised by Teresa Santos Silva and Maria João Romão.

Duarte, M, Carvalho AL, Ferreira MC, Caires B, Romão MJ, Prates JAM, Najmudin S, Bayer EA, Fontes CMGA, Bule P.  2025.  Tripartite binding mode of cohesin-dockerin complexes from Ruminococcus flavefaciens involving naturally truncated dockerins, 2025. 301(7):110325. AbstractWebsite

Polysaccharides in plant cell walls serve as a rich carbon and energy source, yet their structural complexity presents a barrier to efficient degradation. To address this, anaerobic microorganisms like R. flavefaciens have developed sophisticated multi-enzyme complexes known as cellulosomes, which enable the efficient breakdown of these recalcitrant polysaccharides. These complexes are assembled through high-affinity interactions between cohesin (Coh) modules in scaffoldin proteins and dockerin (Doc) modules in cellulosomal enzymes. R. flavefaciens FD-1 harbors one of the most intricate cellulosomes described to date, comprising over 200 Doc-containing proteins encoded in its genome. Despite substantial research on this cellulosome, the role of a group of truncated but functional dockerins, known as group-2 Docs, remains unclear. In this study, we present a detailed structural and binding analysis of a Coh-Doc complex involving the cohesin from the cell-anchoring scaffoldin ScaE and a group-2 Doc that bears only one of the two Ca+2-coordinating loops that characterise the canonical Docs. Our findings reveal a novel tripartite binding mechanism, in which the cohesin can simultaneously bind two distinct dockerin units in three alternative conformations. This discovery provides new insights into the modular versatility of the R. flavefaciens cellulosome and sheds light on the mechanisms that enhance its efficiency in polysaccharide degradation.

XTAL at the 11th ENURS meeting

Past June 6th, XTAL members Maria João Romão, Ana Luísa Carvalho, Cristiano Mota, Guilherme Alves, Fernando Ribeiro, Carolina Videira, Guilherme Oliveira and Marco Graça attended the 11th ENURS meeting (https://www.itqb.unl.pt/meetings-and-courses/enurs), at ITQB-NOVA, Oeiras, Portugal.
MSc student Carolina Videira was selected for Oral Comunication, entitled " Structural insights into the catalytic reduction site of human aldehyde oxidase".

Caseiro, C, McGregor NGS, Alves VD, Carvalho AL, Romão MJ, Davies GJ, Fontes CMGA, Bule P.  2024.  Family GH157 enzyme exhibits broad linkage tolerance and a dual endo/exo- β -glucanase activity on β-glucans, 2024. :137402. AbstractWebsite

The structural and chemical diversity of β-glucans is reflected on the variety of essential biological roles tackled by these polysaccharides. This natural heterogeneity requires an elaborate assortment of enzymatic mechanisms to assemble, degrade or modify, as well as to extract their full biotechnological potential. Recent metagenomic efforts have provided an unprecedented growth in potential new biocatalysts, most of which remain unconfirmed or uncharacterized. Here we report the first biochemical and structural characterization of two bacterial β-glucanases from the recently created glycoside hydrolase family 157 (LaGH157 and BcGH157) and investigate their molecular basis for substrate hydrolysis. Structural analysis by X-ray crystallography revealed that GH157 enzymes belong to clan GH-A, possessing a (β/α)8-barrel fold catalytic domain, two β-sandwich accessory domains and two conserved catalytic glutamates residues, with relative positions compatible with a retaining mechanism of hydrolysis. Specificity screening and enzyme kinetics suggest that the enzymes prefer mixed-linkage glucans over β-1,3-glucans. Activity screening showed that both enzymes exhibit pH optimum at 6.5 and temperature optimum for LaGH157 and BcGH157 at 25 °C and 48 °C, respectively. Product analysis with HPAEC-PAD and LC-MS revealed that both enzymes are endo-1,3(4)-β-glucanases, capable of cleaving β-1,3 and β-1,4-linked glucoses, when preceded by a β-1,3 linkage. Moreover, BcGH157 needs a minimum of 4 subsites occupied for hydrolysis to occur, while LaGH157 only requires 3 subsites. Additionally, LaGH157 possesses exohydrolytic activity on β-1,3 and branching β-1,6 linkages. This unusual bifunctional endo-1,3(4)/exo-1,3–1,6 activity constitutes an expansion on our understanding of β-glucan deconstruction, with the potential to inspire future applications.

Guilherme Vilela-Alves presented his PhD Thesis Plan

Today, our PhD student Guilherme Vilela-Alves, supervised by Cristiano Mota and Maria João Romão, from XTAL, and Harmut Luecke, from the CryoEM group at NOVA FCT, has publicly presented his PhD Thesis Plan. The whole group is proud of you, Guilherme! Great work and stimulating discussion!

The XTAL is back to the European Researchers' Night!

This year's activity was titled: Studying proteins in 3D can help reduce atmospheric CO2

Ana Luísa Carvalho and Cristiano Mota represented the XTAL at ECM34 in Padova

The 34th European Crystallographic Meeting (ECM34,
Oliveira, AR, Mota C, Vilela-Alves G, Manuel RR, Pedrosa N, Fourmond V, Klymanska K, Léger C, Guigliarelli B, Romão MJ, Cardoso Pereira IA.  2024.  An allosteric redox switch involved in oxygen protection in a CO2 reductase, 2024. Nat Chem Biol. 20(1):111-119. AbstractWebsite

Metal-dependent formate dehydrogenases reduce CO2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O2 exposure.