4REP

Crystal Structure of gamma-carotenoid desaturase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of 1'-OH-carotenoid 3,4-desaturase from Nonlabens dokdonensis DSW-6.

Ahn, J.W.Kim, K.J.

(2015) Enzyme Microb Technol 77: 29-37

  • DOI: 10.1016/j.enzmictec.2015.05.005
  • Primary Citation of Related Structures:  
    4REP

  • 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 ...

    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.


    Organizational Affiliation

    School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, South Korea. Electronic address: kkim@knu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-carotene desaturaseA495Nonlabens dokdonensis DSW-6Mutation(s): 0 
Gene Names: DDD_2394crtD
EC: 1.3.99 (PDB Primary Data), 1.3.99.27 (UniProt)
UniProt
Find proteins for L7WC64 (Nonlabens dokdonensis (strain DSM 17205 / KCTC 12402 / DSW-6))
Explore L7WC64 
Go to UniProtKB:  L7WC64
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.369α = 90
b = 72.835β = 110.29
c = 68.137γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description