Abstract
Metallosphaera sedula is a thermoacidophilic autotrophic archaeon known to utilize the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle) as carbon fixation pathway. 3-Hydroxypropionyl-CoA dehydratase (3HPCD) is an enzyme involved in the 3-HP/4-HB cycle by converting 3-hydroxypropionyl-CoA to acryloyl-CoA. To elucidate the molecular mechanism of 3HPCD from M. sedula (Ms3HPCD), we determined its crystal structure in complex with Coenzyme A (CoA). Ms3HPCD showed an overall structure and the CoA-binding mode similar to other enoyl-CoA hydratase (ECH) family enzymes. However, compared with the other ECHs, Ms3HPCD has a tightly formed α3 helix near the active site, and bulky aromatic residues are located at the enoyl-group binding site, resulting in the enzyme having an optimal substrate binding site for accepting short-chain 3-hydroxyacyl-CoA as a substrate. Moreover, based on the phylogenetic tree analysis, we propose that the 3HPCD homologues from the phylum Crenarchaeota have an enoyl-group binding pocket similar to that of bacterial short-chain ECHs.
Highlights
The 3-HP/4-HB cycle is largely divided into two sub-pathways, the 3-HP sub-pathway and the 4-HB sub-pathway (Fig. 1a)
We report the first crystal structure of 3-hydroxypropionyl-CoA dehydratase (3-HPCD) from M. sedula (Ms3HPCD) in complex with Coenzyme A (CoA), and reveal how the enzyme accommodates 3-HP-CoA as a substrate
The monomeric structure of Ms3HPCD consists of three distinct domains: One spiral domain and two trimerization domains (Fig. 2a)
Summary
Metallosphaera sedula is a thermoacidophilic autotrophic archaeon known to utilize the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle) as carbon fixation pathway. 3-Hydroxypropionyl-CoA dehydratase (3HPCD) is an enzyme involved in the 3-HP/4-HB cycle by converting 3-hydroxypropionyl-CoA to acryloyl-CoA. In the 3-HP sub-pathway, acetyl-CoA is converted to succinyl-CoA by the addition of two molecules of bicarbonate (Fig. 1a). This sub-pathway consists of nine enzymes, including 3-hydroxypropionyl-CoA dehydratase (3-HPCD)[10,12,19,20,21]. In the 4-HB sub-pathway, succinyl-CoA is converted into two molecules of acetyl-CoA through seven enzymatic reactions (Fig. 1a)[10,12,19,20,21]. We report the first crystal structure of 3-HPCD from M. sedula (Ms3HPCD) in complex with CoA, and reveal how the enzyme accommodates 3-HP-CoA as a substrate. Through structural comparisons with other ECH enzymes, we provide insights into how the protein accommodates only short chain hydroxyacyl-CoA as a substrate
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