4OKM | pdb_00004okm

Selinadiene Synthase apo and in complex with diphosphate

• PDB DOI: https://doi.org/10.2210/pdb4OKM/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces pristinaespiralis ATCC 25486
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-22 Released: 2014-06-11 
• Deposition Author(s): Baer, P., Rabe, P., Fischer, K., Citron, C.A., Klapschinski, T., Groll, M., Dickschat, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.203 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

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

• PubMed: 24890698 
• DOI: https://doi.org/10.1002/anie.201403648
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 165.89 kDa 
• Atom Count: 11,527 
• Modeled Residue Count: 1,344 
• Deposited Residue Count: 1,460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terpene synthase metal-binding domain-containing protein	A, B, C, D	365	Streptomyces pristinaespiralis ATCC 25486	Mutation(s): 0  Gene Names: SSDG_02809, ZP_06911744 EC: 2.5.1.21 (PDB Primary Data), 4.2.3.181 (UniProt)
UniProt
Find proteins for B5HDJ6 (Streptomyces pristinaespiralis (strain ATCC 25486 / DSM 40338 / CBS 914.69 / JCM 4507 / KCC S-0507 / NBRC 13074 / NRRL 2958 / 5647)) Explore B5HDJ6  Go to UniProtKB:  B5HDJ6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPV	H [auth A], L [auth B], P [auth C]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
MG	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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.203 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.78	α = 90
b = 119.09	β = 90
c = 186.1	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-11 
Deposition Author(s): Baer, P., Rabe, P., Fischer, K., Citron, C.A., Klapschinski, T., Groll, M., Dickschat, J.S.

Revision History  

• 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: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description