8WKL

Rauvolfia serpentina strictosidine synthase (RsSTR) in complex with a non-reactive tryptamine substitute crystallized in P1211 space group

Summary for 8WKL

• Entry DOI: 10.2210/pdb8wkl/pdb
• Descriptor: Strictosidine synthase, 2-(2-methyl-1H-indol-3-yl)ethanamine, DI(HYDROXYETHYL)ETHER, ... (4 entities in total)
• Functional Keywords: beta-propeller fold, bisubstrate enzyme, pictet-spengler reaction, non-substrate anlaog, lyase
• Biological source: Rauvolfia serpentina (serpentwood)
• Total number of polymer chains: 8
• Total formula weight: 285082.38

Authors

Nitin, K.,Rajakumara, E. (deposition date: 2023-09-28, release date: 2024-02-28, Last modification date: 2024-11-20)

Primary citation

Nitin, K.,Rajakumara, E.
Proxy-approach in understanding the bisubstrate activity of strictosidine synthases.
Int.J.Biol.Macromol., 262:130091-130091, 2024

PubMed Abstract: Besides tryptamine (1) and secologanin (2), non-cognate substrates also undergo a Pictet-Spengler reaction (PSR) catalyzed by strictosidine synthases (STR) with differing catalytic properties. We characterized the bisubstrate binding aspect of catalysis - order, affinity, and cooperativity - with STR orthologs from Rauvolfia serpentina (RsSTR) and Ophiorrhiza pumila (OpSTR) by an isothermal titration calorimetry (ITC) based 'proxy approach' that employed a non-reactive tryptamine analog (m1) to capture its inert ternary complexes with STRs and (2). ITC studies with OpSTR and (2) revealed 'tryptamine-first' cooperative binding with (1) and a simultaneous cooperative binding with (m1). Binding cooperativity among (m1) and (2) towards OpSTR was higher than RsSTR. Crystallographic study of RsSTR-(m1) complex helped to understand the unreactive binding of (m1) in terms of orientation and interactions in the RsSTR pocket. PSR with (m1) was revealed to be energetically unfeasible by the density functional theory (DFT) scans of the first hydrogen abstraction by RsSTR. The effect of pH on the bisubstrate binding to OpSTR was deciphered by molecular dynamics simulations (MDS), which also provided a molecular basis for the stability of complex of OpSTR with (m1) and (2). Therefore, we investigated STRs from a substrate binding perspective to inform drug-design and rational enzyme engineering efforts.

PubMed: 38354931
DOI: 10.1016/j.ijbiomac.2024.130091

Experimental method

X-RAY DIFFRACTION (2.67 Å)