6SBC | pdb_00006sbc

Structure of type II terpene cyclase MstE from Scytonema in complex with farnesyl dihydroxybenzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.153 (Depositor), 0.153 (DCC) 
  • R-Value Work: 
    0.115 (Depositor), 0.111 (DCC) 
  • R-Value Observed: 
    0.117 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6SBC

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

A monodomain class II terpene cyclase assembles complex isoprenoid scaffolds.

Moosmann, P.Ecker, F.Leopold-Messer, S.Cahn, J.K.B.Dieterich, C.L.Groll, M.Piel, J.

(2020) Nat Chem 12: 968-972

  • DOI: https://doi.org/10.1038/s41557-020-0515-3
  • Primary Citation Related Structures: 
    6SBB, 6SBC, 6SBD, 6SBE, 6SBF, 6SBG

  • PubMed Abstract: 

    Class II terpene cyclases, such as oxidosqualene and squalene-hopene cyclases, catalyse some of the most complex polycyclization reactions. They minimally exhibit a β,γ-didomain architecture that has been evolutionarily repurposed in a wide range of terpene-processing enzymes and likely resulted from a fusion of unidentified monodomain proteins. Although single domain class I terpene cyclases have already been identified, the corresponding class II counterparts have not been previously reported. Here we present high-resolution X-ray structures of a monodomain class II cyclase, merosterolic acid synthase (MstE). With a minimalistic β-domain architecture, this cyanobacterial enzyme is able to construct four rings in cytotoxic meroterpenoids with a sterol-like topology. The structures with bound substrate, product, and inhibitor provide detailed snapshots of a cyclization mechanism largely governed by residues located in a noncanonical enzyme region. Our results complement the few known class II cyclase crystal structures, while also indicating that archaic monodomain cyclases might have already catalyzed complex reaction cascades.


  • Organizational Affiliation
    • Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 41.2 kDa 
  • Atom Count: 3,128 
  • Modeled Residue Count: 352 
  • Deposited Residue Count: 367 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MstE367Scytonema sp. PCC 10023Mutation(s): 0 
Gene Names: mstE
UniProt
Find proteins for A0A2D1CM82 (Scytonema sp. PCC 10023)
Explore A0A2D1CM82 
Go to UniProtKB:  A0A2D1CM82
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D1CM82
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L4H
(Subject of Investigation/LOI)

Query on L4H



Download:Ideal Coordinates CCD File
B [auth A]farnesyl dihydroxybenzoate
C22 H30 O4
VWHKYMBCXCSQEZ-BTMZFSHUSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.153 (Depositor), 0.153 (DCC) 
  • R-Value Work:  0.115 (Depositor), 0.111 (DCC) 
  • R-Value Observed: 0.117 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.98α = 90
b = 77.42β = 90
c = 90.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland205321_165695
Swiss National Science FoundationSwitzerland205320_185077

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-10-14
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description