Difference between revisions of "Part:BBa K535002"

Revision as of 08:56, 19 October 2016

HydA (hydrogenase I)-> Clostridium acetobutylicum ATCC 824

Hydrogenases are a class of metalloenzymes that catalyze the reversible reduction of protons to molecular hydrogen 2H⁺ + 2e⁻ ↔ H₂ with an equilibrium constant that is dependent on the reducing potential of electrons carried by their redox partner.

These metalloenzymes (containing metallo-catalytic clusters) are subdivided into two classes depending of the two metal atoms that are present at their active center: either a Ni and a Fe atom in the [NiFe]hydrogenases, or two Fe atoms in the [FeFe]hydrogenases. These two forms are phylogenetically distinct, which suggests that hydrogenase function is the result of convergent evolution.

[NiFe] hydrogenases are found across a variety of organisms, [FeFe] hydrogenases are typically restricted to algal species and to a few anaerobic prokaryotes, such as clostridia and sulfate reducers, but are excluded from all cyanobacteria examined to date.

Although [NiFe] and [Fe] hydrogenases are genetically unrelated, similarities between the proteins do exist. First, the active sites of both enzymes contain CO and CN ligands, and, second, each active site contains a binuclear metal center.

The hydrogenase presented here is a [FeFe] hydrogenase from Clostridium acetobutylicum ATCC 824 which is a Gram-positive bacteria that belongs to the Firmicutes division and that is an obligate anaerobe capable of produce endospores.

We choose this hydrogenase because [FeFe]-hydrogenases, such as those from Clostridium species contain several “ferredoxin-like” domains. It is speculated that these domains arose through ancestral gene fusions, enhancing hydrogenase interaction with other ferredoxins, and providing an electron transport channel towards the hydrogenase active site.

Because ferredoxin proteins may carry electrons with reducing potentials closer to that of the H₂/H⁺ pair (−420 mV), [FeFe]-hydrogenases thermodynamically favor hydrogen production relative to [NiFe] hydrogenases, which are generally coupled to NAD(P)H, with a reducing potential of -320 mV and are frequently regarded as predominantly H₂ uptake enzymes.

[Fe] hydrogenase catalytic site is known as the H-cluster and consists of a [4Fe4S] cluster connected through a bridging cysteinyl ligand to a binuclear [2Fe] center. In addition to binding CO and CN, the iron atoms of the [2Fe] center coordinate a bridging organic group thought to be a di(thio-methyl)amine moiety. The H-clusters of [Fe] hydrogenases are easily oxidized and are located in the interior of the protein structure. These sites are connected to the surface by a hydrophobic channel that facilitates H₂ diffusion.

Because of the complexity of the [Fe] hydrogenase H-cluster assembly, the active hydrogenase expression require at least three accessory proteins called the HydE, HydF (part HydEF), and HydG (part HydG) maturases, like the [FeFe] hydrogenases, HydE, HydF, and HydG also require ISCs (iron-sulfur clusters).

The reduced nature of the H-cluster and accessory iron-sulfur clusters (ISCs) makes the Hydrogenase and the maturases susceptible to damage by O₂ oxidation.

Also, Group iGEM16_ShanghaitechChina have optimized the coding sequence of HydA (Part No. BBa_K2132004, https://parts.igem.org/Part:BBa_K2132004) through the following parameters without changing their amino acids sequence: Codon usage bias, GC content, CpG dinucleotides content, mRNA secondary structure, Cryptic splicing sites, Premature PolyA sites, Internal chi sites and ribosomal binding sites, Negative CpG islands, RNA instability motif (ARE), Repeat sequences (direct repeat, reverse repeat, and Dyad repeat). The new parts also have modified with Histag and SpyTag for other convenient usages.

Sequence and Features