7S3T

NzeB Diketopiperazine Dimerase Mutant: Q68I-G87A-A89G-I90V

Summary for 7S3T

• Entry DOI: 10.2210/pdb7s3t/pdb
• Descriptor: NascB, PROTOPORPHYRIN IX CONTAINING FE, (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione, ... (6 entities in total)
• Functional Keywords: cytochrome p450, diketopiperazine dimerase, natural products, biosynthetic protein
• Biological source: Streptomyces sp.
• Total number of polymer chains: 1
• Total formula weight: 45165.08

Authors

Harris, N.R.,Shende, V.V.,Sanders, J.N.,Newmister, S.A.,Khatri, Y.,Movassaghi, M.,Houk, K.N.,Sherman, D.H. (deposition date: 2021-09-08, release date: 2022-10-05, Last modification date: 2023-11-15)

Primary citation

Shende, V.V.,Harris, N.R.,Sanders, J.N.,Newmister, S.A.,Khatri, Y.,Movassaghi, M.,Houk, K.N.,Sherman, D.H.
Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases.
Angew.Chem.Int.Ed.Engl., 2023

PubMed Abstract: In the biosynthesis of the tryptophan-linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high-resolution crystal structure of selective Csp -N bond forming dimerase, AspB. Overlay of the AspB structure onto C-C and C-N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities. Molecular dynamics (MD) simulations identified a region of NzeB with increased conformational flexibility relative to AspB, and interchange of this region along with a single active site mutation led to a variant that catalyzes exclusive C-N bond formation. MD simulations also suggest that intermolecular C-C or C-N bond formation results from a change in mechanism, supported experimentally through use of a substrate mimic.

PubMed: 36610039
DOI: 10.1002/anie.202210254

Experimental method

X-RAY DIFFRACTION (1.4 Å)