4REP

Crystal Structure of gamma-carotenoid desaturase

Summary for 4REP

• Entry DOI: 10.2210/pdb4rep/pdb
• Descriptor: Gamma-carotene desaturase, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... (4 entities in total)
• Functional Keywords: rossmann fold, fad-binding, oxidoreductase, flavoprotein, desaturase, gamma-carotenoid desaturase
• Biological source: Nonlabens dokdonensis DSW-6
• Total number of polymer chains: 1
• Total formula weight: 56787.86

Authors

Ahn, J.-W.,Kim, E.-J.,Kim, S.,Kim, K.-J. (deposition date: 2014-09-23, release date: 2015-07-15, Last modification date: 2024-02-28)

Primary citation

Ahn, J.W.,Kim, K.J.
Crystal structure of 1'-OH-carotenoid 3,4-desaturase from Nonlabens dokdonensis DSW-6.
Enzyme.Microb.Technol., 77:29-37, 2015

PubMed Abstract: The γ-carotenoids, such as myxol and saproxanthin, have a high potential to be utilized in nutraceutical and pharmaceutical industries for their neuro-protective and antioxidant effects. CrtD is involved in the production of γ-carotenoids by desaturating the C3'-C4' position of 1'-OH-γ-carotenoid. We determined the crystal structure of CrtD from Nonlabens dokdonensis DSW-6 (NdCrtD), the first structure of CrtD family enzymes. The NdCrtD structure was composed of two distinct domains, an FAD-binding domain and a substrate-binding domain, and the substrate-binding domain can be divided into two subdomains, a Rossmann fold-like subdomain and a lid subdomain. Although the FAD-binding domain showed a structure similar to canonical FAD-containing enzymes, the substrate-binding domain exhibited a novel structure to constitute a long and hydrophobic tunnel with a length of ∼40 Å. The molecular docking-simulation reveals that the tunnel provides an appropriate substrate-binding site for the carotenoid such as 1'-OH-γ-carotene with a length of ∼35 Å. We could predict residues related to recognize the 1'-hydroxyl group and to stabilize the hydrophobic end without hydroxyl group. Moreover, we suggest that the flexible entrance loop may undergo an open-closed formational change during the binding of the substrate.

PubMed: 26138397
DOI: 10.1016/j.enzmictec.2015.05.005

Experimental method

X-RAY DIFFRACTION (1.97 Å)