9QZ4

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493D structure in complex with substrate 2-HIB-CoA and inactive cofactor 3-deaza-ThDP

Summary for 9QZ4

• Entry DOI: 10.2210/pdb9qz4/pdb
• Descriptor: 2-hydroxyacyl-CoA lyase, 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE, S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2-hydroxy-2-methylpropanethioate, ... (5 entities in total)
• Functional Keywords: thdp, coa, hacl, lyase
• Biological source: Actinomycetospora chiangmaiensis DSM 45062
• Total number of polymer chains: 2
• Total formula weight: 133347.34

Authors

Zahn, M.,Rohwerder, T. (deposition date: 2025-04-22, release date: 2026-02-04)

Primary citation

Zahn, M.,Seroka, B.,Lazny, R.,Lotowski, Z.,Rohwerder, T.
C2 alpha-carbanion-protonating glutamate discloses tradeoffs between substrate accommodation and reaction rate in actinobacterial 2-hydroxyacyl-CoA lyase.
Febs Open Bio, 2026

PubMed Abstract: Thiamine-dependent actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) catalyzes the reversible cleavage of 2-hydroxyacyl-CoAs to formyl-CoA and carbonyl compounds. To exploit the enzyme's biotechnological potential, a deeper understanding of the catalysis is required. Previously, AcHACL E493 was identified as an important acid/base catalyst. Here, wild-type and E493 mutant crystal structures representing Michaelis complexes with 2-hydroxyisobutyryl-CoA and (S)-2-methylglyceryl-CoA are provided. Although E493 guarantees high rates of essential proton transfers in AcAHCL-catalyzed on-pathway cleavage of 2-hydroxyacyl-CoAs and off-pathway carboligations with short-chain aldehydes and ketones, wild-type substrate accommodation is suboptimal. Not E493D, but E493A and E493S mutations improved K. However, k is substantially reduced in the mutants. These tradeoffs are discussed by comparing active sites of AcHACL and related enzymes either lacking or possessing an E493 homolog.

PubMed: 41606311
DOI: 10.1002/2211-5463.70199

Experimental method

X-RAY DIFFRACTION (1.63 Å)