NiFe ‐Hydrogenase Assembly

Abstract

[NiFe]‐hydrogenases are ancient enzymes that catalyze the reversible oxidation of dihydrogen. All [NiFe]‐hydrogenases are composed of minimally a catalytic large subunit with a [NiFe]‐cofactor in the active site and an electron‐transferring small subunit, which has an array of iron–sulfur clusters that channel electrons to and from the large subunit. Depending on the organism in which they are found, [NiFe]‐hydrogenases can be membrane‐associated or soluble enzymes. The NiFe(CN) 2 CO‐cofactor is coordinated via four cysteinyl thiolates to the protein backbone. All organisms synthesizing these enzymes possess a conserved set of six hydrogenase pleiotropy (Hyp) proteins that are responsible for synthesis and insertion of the cofactor. Microorganisms that grow in oxygen have additional proteins that serve to protect O 2 ‐labile intermediates of the cofactor during synthesis. HypD has a 4Fe–4S cluster and is the only redox‐active protein on the maturation pathway. It readily interacts with HypC and together, they form the basis of the scaffold upon which the Fe(CN) 2 CO moiety of the cofactor is assembled. The diatomic ligands CO and CN‐ are derived from distinct metabolic intermediates. Both cyanyl moieties are derived from carbamoylphosphate through the combined actions of the carbamoyltransferase HypF and the HypE dehydratase, which form a heterotetrameric complex that can interact with the HypCD complex. HypE generates a (iso)thiocyanate on its C‐terminal cysteinyl residue, and this is transferred by an as yet unknown mechanism to an Fe(I)‐CO group coordinated by the HypCD complex. Current evidence supports the hypothesis that HypC receives an iron ion bound with CO 2 derived from a cellular decarboxylase. Upon interaction with HypD, the CO 2 is proposed to be reduced to CO while directly attached to the Fe. HypD has a thiol/disulfide fold that allows delivery of two electrons and two protons for CO 2 reduction. Neither the source of the electrons on HypD nor the metabolic origins of the Fe and CO 2 on HypC are currently known. After both cyanyl groups are attached to Fe(I)‐CO, HypC of the Hyp complex undergoes a specific interaction with the apo form of the large subunit. In a presumptive thiol‐transferase reaction, the Fe(CN) 2 CO moiety is inserted into the active site cavity, which is somehow held in an open conformation through a key interaction of the C‐terminal peptide on the large subunit with another part of the protein. Insertion of the nickel ion by the HypAB complex, assisted by the peptidyl‐prolyl cis/trans isomerase SlyD, provides the recognition template for a nickel‐dependent and hydrogenase‐specific endoprotease that cleaves the C‐terminal peptide from the large subunit, causing a conformation switch that closes the active site. After the conformational change, the large subunit can interact with the mature small subunit carrying its full complement of iron–sulfur clusters. The heterodimer is then delivered to its final cellular destination, which can be the cytoplasm, as in the case of soluble hydrogenases, or the cytoplasmic membrane in the case of H 2 ‐oxidizing or H 2 ‐producing enzymes.

The N‐terminal domains of the paralogous HycE and NuoCD govern assembly of the respective formate hydrogenlyase and NADH dehydrogenase complexes

“…A similar observation for a Δ hycE strains was made previously . Generally, for hydrogenase assembly to occur, the large subunit must receive its [NiFe]‐cofactor and therefore interact with various delivery proteins and undergo endoproteolytic processing . Only then is the protein primed for interaction with its small subunit, and this allows the subsequent initiation of the assembly of the entire FHL complex.…”

“…These cysteinyl residues are not present in NuoD (Figs and ). Six pleiotropic Hyp proteins are required for synthesis of the [NiFe]‐cofactor including its diatomic ligands attached to the Fe atom . Of these proteins, the HypC and HypA proteins interact directly with HycE for Fe(CN) 2 CO and Ni 2+ insertion, respectively .…”

In Vivo Assembly of a Genetically Encoded Artificial Metalloenzyme for Hydrogen Production

“…The order of metal addition is critical for quantitative assembly of the functional cofactor . Cleavage of a C-terminal extended domain induces proper folding, and binding to the small, [FeS]-cluster containing subunit gives the fully assembled hydrogenase. , The complexity of this pathway coupled with the still-unknown metabolic precursor of the CO ligand on Fe in the standard enzymes and, until recently, a lack of effective in vivo activity screens have hindered efforts to evolve hydrogenases in order to enhance specific activity traits. , …”

Dissection of the Hydrogen Metabolism of the Enterobacterium Trabulsiella guamensis: Identification of a Formate-Dependent and Essential Formate Hydrogenlyase Complex Exhibiting Phylogenetic Similarity to Complex I

“…1A). For example, it contains an endoprotease gene, hyfK, whose gene product is predicted to be required for processing of the large subunit after completion of the metal cofactor insertion and is missing in the E. coli hyf operon (13). Instead, there is no formate transporter FocB encoded within the T. guamensis hyf operon.…”