7QB8

Crystal structure of a cyclodipeptide synthase from Parcubacteria bacterium RAAC4_OD1_1, WT form

Summary for 7QB8

• Entry DOI: 10.2210/pdb7qb8/pdb
• Related: 7QAE 7QAQ 7QAT 7QAU 7QAW 7QAX 7QAY
• Descriptor: Cyclodipeptide synthase (2 entities in total)
• Functional Keywords: cyclodipeptide synthase, ligase
• Biological source: Parcubacteria bacterium RAAC4_OD1_1
• Total number of polymer chains: 1
• Total formula weight: 27334.52

Authors

Sutherland, E.,Harding, C.J.,Czekster, C.M. (deposition date: 2021-11-18, release date: 2022-09-28, Last modification date: 2024-01-31)

Primary citation

Sutherland, E.,Harding, C.J.,Czekster, C.M.
Active site remodelling of a cyclodipeptide synthase redefines substrate scope.
Commun Chem, 5:101-101, 2022

PubMed Abstract: Cyclodipeptide synthases (CDPSs) generate a wide range of cyclic dipeptides using aminoacylated tRNAs as substrates. Histidine-containing cyclic dipeptides have important biological activities as anticancer and neuroprotective molecules. Out of the 120 experimentally validated CDPS members, only two are known to accept histidine as a substrate yielding cyclo(His-Phe) and cyclo(His-Pro) as products. It is not fully understood how CDPSs select their substrates, and we must rely on bioprospecting to find new enzymes and novel bioactive cyclic dipeptides. Here, we developed an in vitro system to generate an extensive library of molecules using canonical and non-canonical amino acids as substrates, expanding the chemical space of histidine-containing cyclic dipeptide analogues. To investigate substrate selection we determined the structure of a cyclo(His-Pro)-producing CDPS. Three consecutive generations harbouring single, double and triple residue substitutions elucidated the histidine selection mechanism. Moreover, substrate selection was redefined, yielding enzyme variants that became capable of utilising phenylalanine and leucine. Our work successfully engineered a CDPS to yield different products, paving the way to direct the promiscuity of these enzymes to produce molecules of our choosing.

PubMed: 36518199
DOI: 10.1038/s42004-022-00715-2

Experimental method

X-RAY DIFFRACTION (1.9 Å)