Fidel Ramírez-Amador

Our latest work on the nitrogenase-like methylthio-alkane reductase, which specifically reduces reduces carbon-sulfide bonds is now out @natcatal.nature.com: doi.org/10.1038/s419.... We find for the first time large #nitrogenase metalloclusters (P- and L-cluster) outside nitrogenases.

Happy to share our latest review article, this time joining forces with 📌Seigo Shima, 📌James Birrell, 📌Giorgio Caserta, and 📌Oli Lenz. We wrote about hydrogenase catalysis because this is what we do best 😎
doi.org/10.1002/9783...

Methanosarcina acetivorans requires methanol:coenzyme M methyltransferases for ethane formation from ethanol - Antonie van Leeuwenhoek Corrinoid-dependent enzymes either catalyze methyltransfer reactions, or they generate substrate radicals using adenosylcobalamin for subsequent rearrangement reactions. The corrinoid-dependent methyl...

#Methanosarcina acetivorans requires methanol:coenzyme M methyltransferases for #ethane formation from ethanol #methane
link.springer.com/article/10.1...

New frontiers in short-chain alkyl-coenzyme M reductases
#methanogenesis #methane #microbiology
www.sciencedirect.com/science/arti...

Carbon monoxide metabolism in freshwater anaerobic methanotrophic archaea https://www.biorxiv.org/content/10.1101/2025.09.16.676500v1

Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications
#microbiology #methane #archaea
@natcomms.nature.com
www.nature.com/articles/s41...

Protein Structural Phylogenetics Abstract. Protein structural phylogenetics is an interdisciplinary branch of molecular evolution that (i) uses 3D structural data to trace evolutionary his

Fantastic review on methodological developments in protein structural phylogenetics
academic.oup.com/gbe/article/...

Stepwise and reversible assembly of [2Fe–2S] rhombs to [8Fe–8S] clusters and their topological interconversions - Nature Chemistry Elucidating the nature of the metallocofactors in nitrogenase enzymes, and preparing synthetic analogues of these clusters, is a classic target for bioinorganic chemists. Now the transformation of [Fe...

Stepwise and reversible assembly of [2Fe–2S] rhombs to [8Fe–8S] clusters (Mougel et al. via @natchem.nature.com)
www.nature.com/articles/s41...

Nanoengineered bioanode with oxygen-insensitive hydrogenase for sustainable energy harvesting from atmospheric hydrogen and waste gases Enzymatic biofuel cells (EBFCs) utilizing hydrogenases to oxidize hydrogen offer a sustainable approach to energy conservation. However, the oxygen se…

1/3 Electricity from air! In the top journal Nano Energy today, we report the first fuel cell that makes power from air alone. We achieved this by using the enzyme Huc to oxidize ambient hydrogen. This results in a continuous low-level power from air and higher outputs with industrial waste gases.

Microbial metal physiology: ions to ecosystems Nature Reviews Microbiology - Metal ions are required for all cells, and their homeostasis relies on ancient mechanisms that facilitate their import, distribution and storage. In this Review,...

Metal ions are universally required for life, and many of the foundational principles of metal homeostasis have emerged from studies of microbial systems. In this review, I provide a introductory overview targeted to those new to the field.
#MicroSky #Metals

rdcu.be/eycU2

Electron flow in hydrogenotrophic methanogens under nickel limitation - Nature Two distantly related methanogens shift the methanogenic pathway under nickel limitation, suggesting that methanogens adapt to changing bioavailability of nickel by rerouting electron flow between two...

Our new study shows how nickel limitation changes electron flow in methanogens.
@nature.com
#methanogens #methane #archaea
www.nature.com/articles/s41...

A general substitution matrix for structural phylogenetics. Abstract. Sequence-based maximum likelihood (ML) phylogenetics is a widely used method for inferring evolutionary relationships, which has illuminated the

New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...

Proud to present the lab's latest work. The full structure of the sodium translocating methyltransferase (Mtr) bound to a small oxygen-responsive small protein MtrI. Work by Tristan and together with @schmitzstreitslab.bsky.social .

www.biorxiv.org/content/10.1101/2025.06.02.657420v1

Clustering for methane - Nature Catalysis Nature Catalysis - Clustering for methane

CLUSTERING FOR METHANE
Nice write-up @natcatal.nature.com of our recent article on MCR activation 🙏🏻
www.nature.com/articles/s41...

Two Key Ferredoxins for Nitrogen Fixation Have Different Specificities and Biophysical Properties Two ferredoxins, FdC and FdN, are collectively essential for the process of nitrogen fixation by the iron nitrogenase in R. capsulatus. We explore the biophysical factors, through spectroscopic and s....

Leveraging spectroscopic and structural approaches we obtained new insights into the role of #ferredoxins in N2 fixation. Just published in Chemistry – A European Journal: doi.org/10.1002/chem...! Great work by Holly Addison. Fantastic collaboration with Antonio Pierik on the EPR characterization.

Happy to present the lab latest work, today from the green-side. The ultimate PSII assembly intermediate that directly precedes incorporation of the Mn4O5Ca cluster and formation of the OEC. Psb32 binds to PsbV, challenging the assumption the extrinsic subunits all associate spontaneously in-vivo.

My lab mates and their collaborators have a really cool paper you should check out: the structure of catalytically active (Ni(I)) methyl-coM reductase: www.biorxiv.org/content/10.1...

Early life – Enzyme for biological methane production decoded

Short press piece @unipotsdam.bsky.social about our new article @nature.com on methyl coenzyme M reductase (MCR)
www.uni-potsdam.de/en/headlines...

Durchbruch in der Methan-Forschung: Aktivierungsmechanismus des Methan-produzierenden Enzyms entschlüsselt „Nature“-Publikation offenbart die evolutionäre Verbindung zwischen zwei fundamentalen biologischen Prozessen

🧪 Durchbruch in der biochemischen Grundlagenforschung mit zentraler Bedeutung für #Energie & #Klima:
Ein Team der @unimarburg.bsky.social & der #TUBerlin/ @unisyscat.bsky.social hat erstmals den Aktivierungsmechanismus des Enzyms MCR aufgeklärt – zentral für die biologische Produktion von #Methan. 👇

This project was possible thanks to the great team formed with my shared co-first authors @sophia-pa.bsky.social and @rnfr2d2.bsky.social and the supervision of @schullerjm.bsky.social plus awesome contributions, specially from @stripplab.bsky.social @georghochberg.bsky.social and Silvan Scheller.

Amazingly, our phylogenetic reconstructions traced the origin of these clusters and their protein scaffolds in methanogens before being repurposed for nitrogen fixation.

Last but not least, three iron-sulfur clusters shape an electron transfer pathway towards the exposed coenzyme F430. Unexpectedly, these clusters are reminiscent of the [8Fe-9S-C] cofactors (or L-clusters) that so far had only been found in the nitrogenase family.

These changes allow CoB-SH to descend and form the heterodisulfide by-product with CoM. Whereas the more distal active site is still rigid while holding the substrates.

But how is the catalytic pocket of MCR remodelled during activation? When complexed to the other components, the more 'proximal' half of MCR undergoes drastic conformational changes to expose the Ni-center in coenzyme F430, likely facilitating its further reduction.

To show the ATP-dependency activation of MCR, we followed the CH4 production at different scenarios (as isolated, ATP depletion, non-hydrolyzable ATP analogues). The external addition of ATP not only boosts the generation of CH4 but also promotes the interaction of A2 with MCR.

We used redox-controlled cryoEM to obtain different functional states (local resolutions as high as 1.8 angstrom!) of the activation complex asymetrically bound to MCR. The small McrC along with several methanogenic marker proteins (Mmp) and A2 (an ATPase) compose the complex.

MCR is one of the most abundant enzymes on Earth and the major biological producer of methane (CH4). However, MCR is only active when its Ni-containing ligand coenzyme F430 is in the Ni(I) state, an energetically expensive process that requires ATP.

I'm truly excited to announce our new publication in @nature.com unraveling a central picture of the Methyl-coenzyme M reductase (MCR) activation machinery and it's strong ATP dependency - kudos to @rnfr2d2.bsky.social for the fantastic illustration!

LINK: www.nature.com/articles/s41...