6D9F

Protein 60 with aldehyde deformylating oxidase activity from Kitasatospora setae

Summary for 6D9F

• Entry DOI: 10.2210/pdb6d9f/pdb
• Descriptor: Putative VlmB homolog, FE (III) ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: ferritin-like, lyase
• Biological source: Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054) (Streptomyces setae)
• Total number of polymer chains: 2
• Total formula weight: 74503.66

Authors

Arenas, R.,Wilson, D.K.,Mak, W.S.,Siegel, J.B. (deposition date: 2018-04-28, release date: 2019-05-08, Last modification date: 2024-03-13)

Primary citation

Mak, W.S.,Wang, X.,Arenas, R.,Cui, Y.,Bertolani, S.,Deng, W.Q.,Tagkopoulos, I.,Wilson, D.K.,Siegel, J.B.
Discovery, Design, and Structural Characterization of Alkane-Producing Enzymes across the Ferritin-like Superfamily.
Biochemistry, 59:3834-3843, 2020

PubMed Abstract: To complement established rational and evolutionary protein design approaches, significant efforts are being made to utilize computational modeling and the diversity of naturally occurring protein sequences. Here, we combine structural biology, genomic mining, and computational modeling to identify structural features critical to aldehyde deformylating oxygenases (ADOs), an enzyme family that has significant implications in synthetic biology and chemoenzymatic synthesis. Through these efforts, we discovered latent ADO-like function across the ferritin-like superfamily in various species of Bacteria and Archaea. We created a machine learning model that uses protein structural features to discriminate ADO-like activity. Computational enzyme design tools were then utilized to introduce ADO-like activity into the small subunit of class I ribonucleotide reductase. The integrated approach of genomic mining, structural biology, molecular modeling, and machine learning has the potential to be utilized for rapid discovery and modulation of functions across enzyme families.

PubMed: 32935984
DOI: 10.1021/acs.biochem.0c00665

Experimental method

X-RAY DIFFRACTION (2.03 Å)