4N5L

Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase from Ralstonia eutropha

Summary for 4N5L

• Entry DOI: 10.2210/pdb4n5l/pdb
• Related: 1q7b 3vzp 4N5M 4N5N
• Descriptor: Acetoacetyl-CoA reductase (2 entities in total)
• Functional Keywords: alpha/beta structure, oxidoreductase
• Biological source: Ralstonia eutropha
• Cellular location: Cytoplasm: P14697
• Total number of polymer chains: 2
• Total formula weight: 58798.32

Authors

Kim, J.-E.,Kim, S.,Kim, K.-J. (deposition date: 2013-10-10, release date: 2013-12-11, Last modification date: 2023-11-08)

Primary citation

Kim, J.-E.,Chang, J.H.,Kim, E.-J.,Kim, K.-J.
Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase PhaB from Ralstonia eutropha
Biochem.Biophys.Res.Commun., 443:783-788, 2014

PubMed Abstract: (R)-3-hydroxybutyryl-CoA dehydrogenase PhaB from Ralstonia eutropha H16 (RePhaB) is an enzyme that catalyzes the NADPH-dependent reduction of acetoacetyl-CoA, an intermediate of polyhydroxyalkanoates (PHA) synthetic pathways. Polymeric PHA is used to make bioplastics, implant biomaterials, and biofuels. Here, we report the crystal structures of RePhaB apoenzyme and in complex with either NADP(+) or acetoacetyl-CoA, which provide the catalytic mechanism of the protein. RePhaB contains a Rossmann fold and a Clamp domain for binding of NADP(+) and acetoacetyl-CoA, respectively. The NADP(+)-bound form of RePhaB structure reveals that the protein has a unique cofactor binding mode. Interestingly, in the RePhaB structure in complex with acetoacetyl-CoA, the conformation of the Clamp domain, especially the Clamp-lid, undergoes a large structural change about 4.6 Å leading to formation of the substrate pocket. These structural observations, along with the biochemical experiments, suggest that movement of the Clamp-lid enables the substrate binding and ensures the acetoacetyl moiety is located near to the nicotinamide ring of NADP(+).

PubMed: 24211201
DOI: 10.1016/j.bbrc.2013.10.150

Experimental method

X-RAY DIFFRACTION (1.65 Å)