6RT8 | pdb_00006rt8

Structure of catharanthine synthase - an alpha-beta hydrolase from Catharanthus roseus with a cleaviminium intermediate bound

PDB DOI: https://doi.org/10.2210/pdb6RT8/pdb

Classification: HYDROLASE
Organism(s): Catharanthus roseus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-05-22 Released: 2020-03-04
Deposition Author(s): Caputi, L., Franke, J., Bussey, K., Farrow, S.C., Curcino Vieira, I.J., Stevenson, C.E.M., Lawson, D.M., O'Connor, S.E.
Funding Organization(s): European Research Council, Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.234 (Depositor), 0.238 (DCC)
R-Value Work:
0.194 (Depositor), 0.202 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis of cycloaddition in biosynthesis of iboga and aspidosperma alkaloids.

Caputi, L., Franke, J., Bussey, K., Farrow, S.C., Vieira, I.J.C., Stevenson, C.E.M., Lawson, D.M., O'Connor, S.E.

(2020) Nat Chem Biol 16: 383-386

PubMed: 32066966 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41589-019-0460-x
Primary Citation Related Structures:
6RJ8, 6RS4, 6RT8

PubMed Abstract:
Cycloaddition reactions generate chemical complexity in a single step. Here we report the crystal structures of three homologous plant-derived cyclases involved in the biosynthesis of iboga and aspidosperma alkaloids. These enzymes act on the same substrate, named angryline, to generate three distinct scaffolds. Mutational analysis reveals how these highly similar enzymes control regio- and stereo-selectivity.

Organizational Affiliation

Max Planck Institute of Chemical Ecology, Department of Natural Product Biosynthesis, Jena, Germany.

Macromolecule Content

Total Structure Weight: 300.44 kDa
Atom Count: 20,132
Modeled Residue Count: 2,501
Deposited Residue Count: 2,640
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catharanthine synthase	A, B, C, D, E A, B, C, D, E, F, G, H	330	Catharanthus roseus	Mutation(s): 0 Gene Names: CS, HL1, Caros025416 EC: 4 (PDB Primary Data), 5.5.1.37 (UniProt)
UniProt
Find proteins for A0A2P1GIW2 (Catharanthus roseus) Explore A0A2P1GIW2 Go to UniProtKB: A0A2P1GIW2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2P1GIW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KJE (Subject of Investigation/LOI) Query on KJE Download:Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain R [auth G] SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain S [auth H] MOL2 format, chain R [auth G] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain S [auth H] mmCIF format, chain R [auth G] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] L [auth C] N [auth D] O [auth E] I [auth A], K [auth B], L [auth C], N [auth D], O [auth E], Q [auth F], R [auth G], S [auth H]	18-carboxymethoxy-cleaviminium C₂₁ H₂₅ N₂ O₂ ULODILYUCKTWMV-CGTJXYLNSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth H]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain T [auth H] SDF format, chain P [auth E] SDF format, chain M [auth C] SDF format, chain J [auth A] MOL2 format, chain T [auth H] MOL2 format, chain P [auth E] MOL2 format, chain M [auth C] MOL2 format, chain J [auth A] mmCIF format, chain T [auth H] mmCIF format, chain P [auth E] mmCIF format, chain M [auth C] mmCIF format, chain J [auth A]	J [auth A], M [auth C], P [auth E], T [auth H]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth E] Focus chain T [auth H] Interactions & Density Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth E] Focus chain T [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.234 (Depositor), 0.238 (DCC)
R-Value Work: 0.194 (Depositor), 0.202 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.54	α = 90
b = 121.03	β = 99.02
c = 157.98	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-04

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council	Belgium	788301
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/P012523/1

Revision History (Full details and data files)

Version 1.0: 2020-03-04
Type: Initial release
Version 1.1: 2020-04-01
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description