Abstract
Accelerated CO2 sequestration uses carbonic anhydrases (CAs) as catalysts; thus, there is much research on these enzymes. The γ-CA from Escherichia coli (EcoCA-γ) was the first γ-CA to display an active site that switches between “open” and “closed” states through Zn2+ coordination by the proton-shuttling His residue. Here, we explored this occurrence in γ-CAs from hydrothermal vent bacteria and also the γ-CA from Methanosarcina thermophila (Cam) using molecular dynamics. Ten sequences were analyzed through multiple sequence alignment and motif analysis, along with three others from a previous study. Conservation of residues and motifs was high, and phylogeny indicated a close relationship amongst the sequences. All structures, like EcoCA-γ, had a long loop harboring the proton-shuttling residue. Trimeric structures were modeled and simulated for 100 ns at 423 K, with all the structures displaying thermostability. A shift between “open” and “closed” active sites was observed in the 10 models simulated through monitoring the behavior of the His proton-shuttling residue. Cam, which has two Glu proton shuttling residues on long loops (Glu62 and Glu84), also showed an active site switch affected by the first Glu proton shuttle, Glu62. This switch was thus concluded to be common amongst γ-CAs and not an isolated occurrence.
Highlights
Carbonic anhydrases (CAs) are fast catalysts for the interconversion of carbon dioxide (CO2) to bicarbonate ions (HCO3−) [1] and, for this reason, have been considered as ideal CO2 sequestration agents
A total of 10 γ-CA sequences from hydrothermal vent bacteria belonging to the class Campylobacteria were retrieved from NCBI (Table 1)
The 10 CAs selected were from Caminibacter mediatlanticus [42], Hydrogenimonas thermophila [43], Lebetimonas natsushimae [44], Epsilonproteobacteria bacterium 4484_65 [45], Nautilia profundicola [46], Nitratiruptor tergarcus [47], Sulfurovum lithotrophicum [48], Sulfurimonas autotrophica [49,50], Sulfurovum sp
Summary
Carbonic anhydrases (CAs) are fast catalysts for the interconversion of carbon dioxide (CO2) to bicarbonate ions (HCO3−) [1] and, for this reason, have been considered as ideal CO2 sequestration agents. Eight different CA classes have been discovered, and these include the α-, β-, γ-, δ-, η-, ζ- and θ-CAs and ι-CAs [2,3,4,5,6,7]. They contain a catalytic metal ion in the active site, which is usually zinc (Zn2+), but it has been observed to be iron (Fe2+) or cadmium (Cd2+) in some γ-CAs [8,9,10,11,12]. The resulting nucleophile attacks the CO2 molecule during catalysis in the CO2-binding pocket close to the active site, resulting in the formation of a bicarbonate ion [17]
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