5KAG

Crystal structure of a dioxygenase in the Crotonase superfamily in P21

Summary for 5KAG

• Entry DOI: 10.2210/pdb5kag/pdb
• Related: 5KAH 5KAJ
• Descriptor: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase, [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE, OXYGEN MOLECULE, ... (4 entities in total)
• Functional Keywords: dioxygenase, dpgc, oxidoreductase
• Biological source: Streptomyces toyocaensis
• Total number of polymer chains: 12
• Total formula weight: 590084.96

Authors

Li, K.,Fielding, E.N.,Condurso, H.L.,Bruner, S.D. (deposition date: 2016-06-01, release date: 2017-06-21, Last modification date: 2023-09-27)

Primary citation

Li, K.,Fielding, E.N.,Condurso, H.L.,Bruner, S.D.
Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase.
Acta Crystallogr D Struct Biol, 73:573-580, 2017

PubMed Abstract: 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.

PubMed: 28695857
DOI: 10.1107/S2059798317007045

Experimental method

X-RAY DIFFRACTION (2.456 Å)