3N0G

Crystal Structure of Isoprene Synthase from Grey Poplar Leaves (Populus x canescens) in complex with three Mg2+ ions and dimethylallyl-S-thiolodiphosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 


Literature

Structure of isoprene synthase illuminates the chemical mechanism of teragram atmospheric carbon emission.

Koksal, M., Zimmer, I., Schnitzler, J.P., Christianson, D.W.

(2010) J Mol Biol 402: 363-373

  • DOI: 10.1016/j.jmb.2010.07.009
  • Primary Citation of Related Structures:  
    3N0F, 3N0G

  • PubMed Abstract: 

    • The X-ray crystal structure of recombinant PcISPS (isoprene synthase from gray poplar hybrid Populus×canescens) has been determined at 2.7 Å resolution, and the structure of its complex with three Mg(2+) and the unreactive substrate analogue dimethylallyl-S-thiolodiphosphate has been determined at 2 ...

    The X-ray crystal structure of recombinant PcISPS (isoprene synthase from gray poplar hybrid Populus×canescens) has been determined at 2.7 Å resolution, and the structure of its complex with three Mg(2+) and the unreactive substrate analogue dimethylallyl-S-thiolodiphosphate has been determined at 2.8 Å resolution. Analysis of these structures suggests that the generation of isoprene from substrate dimethylallyl diphosphate occurs via a syn-periplanar elimination mechanism in which the diphosphate-leaving group serves as a general base. This chemical mechanism is responsible for the annual atmospheric emission of 100 Tg of isoprene by terrestrial plant life. Importantly, the PcISPS structure promises to guide future protein engineering studies, potentially leading to hydrocarbon fuels and products that do not rely on traditional petrochemical sources.

    Organizational Affiliation: 

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoprene synthaseA, B555Populus tremula x Populus albaMutation(s): 3 
Gene Names: ISPS
EC: 4.2.3.27
UniProt
Find proteins for Q9AR86 (Populus canescens)
Explore Q9AR86 
Go to UniProtKB:  Q9AR86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AR86
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DST
Query on DST
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.014α = 90
b = 155.014β = 90
c = 143.744γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-10-02
    Changes: Data collection, Non-polymer description, Structure summary