5KAG image
Deposition Date 2016-06-01
Release Date 2017-06-21
Last Version Date 2023-09-27
Entry Detail
PDB ID:
5KAG
Keywords:
Title:
Crystal structure of a dioxygenase in the Crotonase superfamily in P21
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.46 Å
R-Value Free:
0.23
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
Gene (Uniprot):BU52_01220
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L
Chain Length:438
Number of Molecules:12
Biological Source:Streptomyces toyocaensis
Primary Citation
Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase.
Acta Crystallogr D Struct Biol 73 573 580 (2017)
PMID: 28695857 DOI: 10.1107/S2059798317007045

Abstact

The enzyme DpgC is included in the small family of cofactor-independent dioxygenases. The chemistry of DpgC is uncommon as the protein binds and utilizes dioxygen without the aid of a metal or organic cofactor. Previous structural and biochemical studies identified the substrate-binding mode and the components of the active site that are important in the catalytic mechanism. In addition, the results delineated a putative binding pocket and migration pathway for the co-substrate dioxygen. Here, structural biology is utilized, along with site-directed mutagenesis, to probe the assigned dioxygen-binding pocket. The key residues implicated in dioxygen trafficking were studied to probe the process of binding, activation and chemistry. The results support the proposed chemistry and provide insight into the general mechanism of dioxygen binding and activation.

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