6ACQ

Crystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum, apo form

Summary for 6ACQ

• Entry DOI: 10.2210/pdb6acq/pdb
• Related: 6AA8
• Descriptor: 3-hydroxybutyryl-CoA dehydrogenase (2 entities in total)
• Functional Keywords: rossmann fold, oxidoreductase
• Biological source: Clostridium acetobutylicum
• Total number of polymer chains: 6
• Total formula weight: 196758.26

Authors

Takenoya, M.,Taguchi, S.,Yajima, S. (deposition date: 2018-07-27, release date: 2018-11-07, Last modification date: 2023-11-22)

Primary citation

Takenoya, M.,Taguchi, S.,Yajima, S.
Crystal structure and kinetic analyses of a hexameric form of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum.
Acta Crystallogr F Struct Biol Commun, 74:733-740, 2018

PubMed Abstract: (S)-3-Hydroxybutyryl-CoA dehydrogenase (HBD) has been gaining increased attention recently as it is a key enzyme in the enantiomeric formation of (S)-3-hydroxybutyryl-CoA [(S)-3HB-CoA]. It converts acetoacetyl-CoA to (S)-3HB-CoA in the synthetic metabolic pathway. (S)-3HB-CoA is further modified to form (S)-3-hydroxybutyrate, which is a source of biodegradable polymers. During the course of a study to develop biodegradable polymers, attempts were made to determine the crystal structure of HBD from Clostridium acetobutylicum (CacHBD), and the crystal structures of both apo and NAD-bound forms of CacHBD were determined. The crystals belonged to different space groups: P222 and P2. However, both structures adopted a hexamer composed of three dimers in the asymmetric unit, and this oligomerization was additionally confirmed by gel-filtration column chromatography. Furthermore, to investigate the catalytic residues of CacHBD, the enzymatic activities of the wild type and of three single-amino-acid mutants were analyzed, in which the Ser, His and Asn residues that are conserved in the HBDs from C. acetobutylicum, C. butyricum and Ralstonia eutropha, as well as in the L-3-hydroxyacyl-CoA dehydrogenases from Homo sapiens and Escherichia coli, were substituted by alanines. The S117A and N188A mutants abolished the activity, while the H138A mutant showed a slightly lower K value and a significantly lower k value than the wild type. Therefore, in combination with the crystal structures, it was shown that His138 is involved in catalysis and that Ser117 and Asn188 may be important for substrate recognition to place the keto group of the substrate in the correct position for reaction.

PubMed: 30387779
DOI: 10.1107/S2053230X18014814

Experimental method

X-RAY DIFFRACTION (2.5 Å)