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 33CR | pdb_000033cr

Grimophan Synthase from Variovorax boronicumulans (GriS): open conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.234 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 33CR

This is version 1.1 of the entry. See complete history. 

Literature

Structural Basis of Cyclized C17 Precursor Recognition and Product Formation in Chlororaphen and Grimophan Biosynthesis.

Yang, K., Groll, M., Dickschat, J.S.

(2026) J Am Chem Soc 148: 41698-41706

  • DOI: https://doi.org/10.1021/jacs.6c17074
  • Primary Citation Related Structures: 
    33CR, 33CT, 33CU, 33CV

  • PubMed Abstract: 

    Terpene cyclases (TCs) typically transform acyclic oligoprenyl pyrophosphates through carbocationic cyclization cascades. However, recently discovered bacterial pathways generate compact, cyclized and stereochemically defined noncanonical intermediates through methyltransferases prior to TC catalysis, raising the question of how these unusual substrates are recognized and converted. Here, we report high-resolution crystal structures of two bacterial C17 class I TCs, Pc-ChloS and Vb-GriS, including a complex with a substrate surrogate that defines recognition of the cyclized precursor α-prechlororaphen pyrophosphate (α-PCPP). Combined with mutagenesis and isotope-labeling experiments, these structures provide a molecular framework for chlororaphen and grimophan biosynthesis. Despite highly similar active-site architectures, reciprocal mutagenesis identifies a single Thr/Leu exchange at position 89 as a major determinant of product partitioning. Together with comparisons to other class I TCs, these findings reveal how a conserved scaffold accommodates cyclized terpene precursors, while subtle active-site changes redirect complex carbocation cascades and product formation.


  • Organizational Affiliation: 
    • Kekulé Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, Bonn53121, Germany.

Macromolecule Content 

  • Total Structure Weight: 37.43 kDa 
  • Atom Count: 2,454 
  • Modeled Residue Count: 293 
  • Deposited Residue Count: 318 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Terpene synthase318Variovorax boronicumulansMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
L [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
M [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.234 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.36α = 90
b = 79.36β = 90
c = 183.97γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGR 1861/13-1

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-30
    Type: Initial release
  • Version 1.1: 2026-11-04
    Changes: Database references