8JE4

Crystal structure of LimF prenyltransferase (H239G/W273T mutant) bound with the thiodiphosphate moiety of farnesyl S-thiolodiphosphate (FSPP)

Summary for 8JE4

• Entry DOI: 10.2210/pdb8je4/pdb
• Descriptor: prenyltransferase, LimF, MAGNESIUM ION, TRIHYDROGEN THIODIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: ripp, prenylation, abba fold, transferase
• Biological source: Limnothrix sp. CACIAM 69d
• Total number of polymer chains: 2
• Total formula weight: 69553.62

Authors

Hamada, K.,Oguni, A.,Zhang, Y.,Satake, M.,Goto, Y.,Suga, H.,Ogata, K.,Sengoku, T. (deposition date: 2023-05-15, release date: 2023-11-08, Last modification date: 2023-11-22)

Primary citation

Zhang, Y.,Hamada, K.,Satake, M.,Sengoku, T.,Goto, Y.,Suga, H.
Switching Prenyl Donor Specificities of Cyanobactin Prenyltransferases.
J.Am.Chem.Soc., 145:23893-23898, 2023

PubMed Abstract: Prenyltransferases in cyanobactin biosynthesis are of growing interest as peptide alkylation biocatalysts, but their prenylation modes characterized so far have been limited to dimethylallylation (C5) or geranylation (C10). Here we engaged in structure-guided engineering of the prenyl-binding pocket of a His--geranyltransferase LimF to modulate its prenylation mode. Contraction of the pocket by a single mutation led to a His--dimethylallyltransferase. More importantly, pocket expansion by a double mutation successfully repurposed LimF for farnesylation (C15), which is an unprecedented mode in this family. Furthermore, the obtained knowledge of the essential residues to construct the farnesyl-binding pocket has allowed for rational design of a Tyr--farnesyltransferase by a triple mutation of a Tyr--dimethylallyltransferase PagF. These results provide an approach to manipulate the prenyl specificity of cyanobactin prenyltransferases, broadening the chemical space covered by this class of enzymes and expanding the toolbox of peptide alkylation biocatalysts.

PubMed: 37877712
DOI: 10.1021/jacs.3c07373

Experimental method

X-RAY DIFFRACTION (2.19 Å)