6RO8

The crystal structure of Acinetobacter radioresistens CYP116B5 heme domain

Summary for 6RO8

• Entry DOI: 10.2210/pdb6ro8/pdb
• Descriptor: Cytochrome P450 RhF, PROTOPORPHYRIN IX CONTAINING FE, HISTIDINE, ... (4 entities in total)
• Functional Keywords: cytochrome p450, monooxygenases, biocatalysis, oxidoreductase
• Biological source: Acinetobacter radioresistens
• Total number of polymer chains: 1
• Total formula weight: 52669.14

Authors

Ciaramella, A.,Catucci, G.,Gilardi, G.,Di Nardo, G. (deposition date: 2019-05-10, release date: 2019-08-28, Last modification date: 2024-01-24)

Primary citation

Ciaramella, A.,Catucci, G.,Gilardi, G.,Di Nardo, G.
Crystal structure of bacterial CYP116B5 heme domain: New insights on class VII P450s structural flexibility and peroxygenase activity.
Int.J.Biol.Macromol., 140:577-587, 2019

PubMed Abstract: Class VII cytochromes P450 are self-sufficient enzymes carrying a phthalate family oxygenase-like reductase domain and a P450 domain fused in a single polypeptide chain. The biocatalytic applications of CYP116B members are limited by the need of the NADPH cofactor and the lack of crystal structures as a starting point for protein engineering. Nevertheless, we demonstrated that the heme domain of CYP116B5 can use hydrogen peroxide as electron donor bypassing the need of NADPH. Here, we report the crystal structure of CYP116B5 heme domain in complex with histidine at 2.6 Å of resolution. The structure reveals the typical P450 fold and a closed conformation with an active site cavity of 284 Å in volume, accommodating a histidine molecule forming a hydrogen bond with the water molecule present as 6th heme iron ligand. MD simulations in the absence of any ligand revealed the opening of a tunnel connecting the active site to the protein surface through the movement of F-, G- and H-helices. A structural alignment with bacterial cytochromes P450 allowed the identification of amino acids in the proximal heme site potentially involved in peroxygenase activity. The availability of the crystal structure provides the bases for the structure-guided design of new biocatalysts.

PubMed: 31430491
DOI: 10.1016/j.ijbiomac.2019.08.141

Experimental method

X-RAY DIFFRACTION (2.6 Å)