4OKZ

Selinadiene Synthase in complex with dihydrofarnesyl pyrophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Induced-fit mechanism in class i terpene cyclases.

Baer, P.Rabe, P.Fischer, K.Citron, C.A.Klapschinski, T.A.Groll, M.Dickschat, J.S.

(2014) Angew Chem Int Ed Engl 53: 7652-7656

  • DOI: 10.1002/anie.201403648
  • Primary Citation of Related Structures:  
    4OKM, 4OKZ

  • PubMed Abstract: 
  • We present crystallographic and functional data of selina-4(15),7(11)-diene synthase (SdS) from Streptomyces pristinaespiralis in its open and closed (ligand-bound) conformation. We could identify an induced-fit mechanism by elucidating a rearrangement of the G1/2 helix-break motif upon substrate binding ...

    We present crystallographic and functional data of selina-4(15),7(11)-diene synthase (SdS) from Streptomyces pristinaespiralis in its open and closed (ligand-bound) conformation. We could identify an induced-fit mechanism by elucidating a rearrangement of the G1/2 helix-break motif upon substrate binding. This rearrangement highlights a novel effector triad comprising the pyrophosphate sensor Arg178, the linker Asp181, and the effector Gly182-O. This structural motif is strictly conserved in class I terpene cyclases from bacteria, fungi, and plants, including epi-isozizaene synthase (3KB9), aristolochene synthase (4KUX), bornyl diphosphate synthase (1N20), limonene synthase (2ONG), 5-epi-aristolochene synthase (5EAT), and taxa-4(5),11(12)-diene synthase (3P5R). An elaborate structure-based mutagenesis in combination with analysis of the distinct product spectra confirmed the mechanistic models of carbocation formation and stabilization in SdS.


    Organizational Affiliation

    Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, TU München (Germany).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Terpene synthase metal-binding domain-containing proteinA, B, C, D365Streptomyces pristinaespiralis ATCC 25486Mutation(s): 0 
Gene Names: SSDG_02809ZP_06911744
EC: 2.5.1.21 (PDB Primary Data), 4.2.3.181 (UniProt)
Find proteins for B5HDJ6 (Streptomyces pristinaespiralis (strain ATCC 25486 / DSM 40338 / CBS 914.69 / JCM 4507 / NBRC 13074 / NRRL 2958 / 5647))
Explore B5HDJ6 
Go to UniProtKB:  B5HDJ6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3E9
Query on 3E9

Download Ideal Coordinates CCD File 
H [auth A], L [auth B], P [auth C], T [auth D](3S,6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl trihydrogen diphosphate
C15 H30 O7 P2
UGQVBUXMCRXOIF-HNRFISLBSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , I [auth B] , J [auth B] , K [auth B] , M [auth C] , N [auth C] , 
E [auth A],  F [auth A],  G [auth A],  I [auth B],  J [auth B],  K [auth B],  M [auth C],  N [auth C],  O [auth C],  Q [auth D],  R [auth D],  S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.09α = 90
b = 117.78β = 90
c = 185.59γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2014-08-06
    Changes: Database references
  • Version 1.3: 2014-08-20
    Changes: Non-polymer description