6OS5

Crystal structure of CymD prenyltransferase complexed with L-tryptophan

Summary for 6OS5

• Entry DOI: 10.2210/pdb6os5/pdb
• Descriptor: CymD prenyltransferase, TRYPTOPHAN, BENZOIC ACID, ... (6 entities in total)
• Functional Keywords: prenyltransferase, tryptophan, indole, biosynthesis, transferase
• Biological source: Salinispora arenicola (strain CNS-205)
• Total number of polymer chains: 3
• Total formula weight: 124140.53

Authors

Roose, B.W.,Christianson, D.W. (deposition date: 2019-05-01, release date: 2019-07-17, Last modification date: 2023-10-11)

Primary citation

Roose, B.W.,Christianson, D.W.
Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD.
Biochemistry, 58:3232-3242, 2019

PubMed Abstract: Indole prenyltransferases catalyze the prenylation of l-tryptophan (l-Trp) and other indoles to produce a diverse set of natural products in bacteria, fungi, and plants, many of which possess useful biological properties. Among this family of enzymes, CymD from catalyzes the reverse N1 prenylation of l-Trp, an unusual reaction given the poor nucleophilicity of the indole nitrogen. CymD utilizes dimethylallyl diphosphate (DMAPP) as the prenyl donor, catalyzing the dissociation of the diphosphate leaving group followed by nucleophilic attack of the indole nitrogen at the tertiary carbon of the dimethylallyl cation. To better understand the structural basis of selective indole N-alkylation reactions in biology, we have determined the X-ray crystal structures of CymD, the CymD-l-Trp complex, and the CymD-l-Trp-DMSPP complex (DMSPP is dimethylallyl -thiolodiphosphate, an unreactive analogue of DMAPP). The orientation of l-Trp with respect to DMSPP reveals how the active site contour of CymD serves as a template to direct the reverse prenylation of the indole nitrogen. Comparison to PriB, a C6 bacterial indole prenyltransferase, offers further insight regarding the structural basis of regioselective indole prenylation. Isothermal titration calorimetry measurements indicate a synergistic relationship between l-Trp and DMSPP binding. Finally, activity assays demonstrate the selectivity of CymD for l-Trp and indole as prenyl acceptors. Collectively, these data establish a foundation for understanding and engineering the regioselectivity of indole prenylation by members of the prenyltransferase protein family.

PubMed: 31251043
DOI: 10.1021/acs.biochem.9b00399

Experimental method

X-RAY DIFFRACTION (1.66 Å)