5DBG image
Deposition Date 2015-08-21
Release Date 2015-11-04
Last Version Date 2023-11-08
Entry Detail
PDB ID:
5DBG
Keywords:
Title:
Crystal Structure of Iridoid Synthase from Cantharanthus roseus in complex with NAD+
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.95 Å
R-Value Free:
0.22
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Iridoid synthase
Chain IDs:A, B
Chain Length:374
Number of Molecules:2
Biological Source:Catharanthus roseus
Ligand Molecules
Primary Citation
Structures of Iridoid Synthase from Cantharanthus roseus with Bound NAD(+) , NADPH, or NAD(+) /10-Oxogeranial: Reaction Mechanisms
Angew.Chem.Int.Ed.Engl. 54 15478 15482 (2015)
PMID: 26768532 DOI: 10.1002/anie.201508310

Abstact

Structures of the iridoid synthase nepetalactol synthase in the presence of NAD(+) , NADPH or NAD(+) /10-oxogeranial were solved. The 10-oxogeranial substrate binds in a transoid-O1-C3 conformation and can be reduced by hydride addition to form the byproduct S-10-oxo-citronellal. Tyr178 Oζ is positioned 2.5 Å from the substrate O1 and provides the second proton required for reaction. Nepetalactol product formation requires rotation about C1-C2 to form the cisoid isomer, leading to formation of the cis-enolate, together with rotation about C4-C5, which enables cyclization and lactol production. The structure is similar to that of progesterone-5β-reductase, with almost identical positioning of NADP, Lys146(147), Tyr178(179), and F342(343), but only Tyr178 and Phe342 appear to be essential for activity. The transoid 10-oxogeranial structure also serves as a model for β-face hydride attack in progesterone 5β-reductases and is of general interest in the context of asymmetric synthesis.

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