7pt4 | pdb_00007pt4
Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with a covalently bound reaction intermediate as well as products formyl-CoA and acetone
Structural highlights
FunctionHACL_ACTC0 A lyase that reversibly degrades 2-hydroxyisobutyryl-CoA (2-HIB-CoA) to acetone and formyl-CoA (PubMed:34952003). Probably also cleaves 2-hydroxy-2-methylbutyryl-CoA to butanone and formyl-CoA. Does not act on 2-hydroxy-2-ethylbutyryl-CoA (Probable). A C-terminal lid closes the active site upon substrate binding, and with residues Leu-127 and Ile-492 restricts the size of the active site cavity so it can only use short-chain (C4 and C5) acyl substrates (PubMed:34952003). Part of a pathway that allows cells to grow on 2-methylpropane-1,2-diol or 2-hydroxyisobutyric acid (2-HIBA) as a sole carbon source (PubMed:32351493).[1] [2] [3] Publication Abstract from PubMedActinobacterial 2-hydroxyacyl-CoA lyase reversibly catalyzes the thiamine diphosphate-dependent cleavage of 2-hydroxyisobutyryl-CoA to formyl-CoA and acetone. This enzyme has great potential for use in synthetic one-carbon assimilation pathways for sustainable production of chemicals, but lacks details of substrate binding and reaction mechanism for biochemical reengineering. We determined crystal structures of the tetrameric enzyme in the closed conformation with bound substrate, covalent postcleavage intermediate, and products, shedding light on active site architecture and substrate interactions. Together with molecular dynamics simulations of the covalent precleavage complex, the complete catalytic cycle is structurally portrayed, revealing a proton transfer from the substrate acyl Cbeta hydroxyl to residue E493 that returns it subsequently to the postcleavage Calpha-carbanion intermediate. Kinetic parameters obtained for mutants E493A, E493Q, and E493K confirm the catalytic role of E493 in the WT enzyme. However, the 10- and 50-fold reduction in lyase activity in the E493A and E493Q mutants, respectively, compared with WT suggests that water molecules may contribute to proton transfer. The putative catalytic glutamate is located on a short alpha-helix close to the active site. This structural feature appears to be conserved in related lyases, such as human 2-hydroxyacyl-CoA lyase 2. Interestingly, a unique feature of the actinobacterial 2-hydroxyacyl-CoA lyase is a large C-terminal lid domain that, together with active site residues L127 and I492, restricts substrate size to </=C5 2-hydroxyacyl residues. These details about the catalytic mechanism and determinants of substrate specificity pave the ground for designing tailored catalysts for acyloin condensations for one-carbon and short-chain substrates in biotechnological applications. Mechanistic details of the actinobacterial lyase-catalyzed degradation reaction of 2-hydroxyisobutyryl-CoA.,Zahn M, Konig G, Pham HVC, Seroka B, Lazny R, Yang G, Ouerfelli O, Lotowski Z, Rohwerder T J Biol Chem. 2022 Jan;298(1):101522. doi: 10.1016/j.jbc.2021.101522. Epub 2021, Dec 22. PMID:34952003[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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