5LUN

Ethylene Forming Enzyme from Pseudomonas syringae pv. phaseolicola - P1 ultra-high resolution crystal form in complex with iron, N-oxalylglycine and arginine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural and stereoelectronic insights into oxygenase-catalyzed formation of ethylene from 2-oxoglutarate.

Zhang, Z., Smart, T.J., Choi, H., Hardy, F., Lohans, C.T., Abboud, M.I., Richardson, M.S.W., Paton, R.S., McDonough, M.A., Schofield, C.J.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 4667-4672

  • DOI: 10.1073/pnas.1617760114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Ethylene is important in industry and biological signaling. In plants, ethylene is produced by oxidation of 1-aminocyclopropane-1-carboxylic acid, as catalyzed by 1-aminocyclopropane-1-carboxylic acid oxidase. Bacteria catalyze ethylene production, b ...

    Ethylene is important in industry and biological signaling. In plants, ethylene is produced by oxidation of 1-aminocyclopropane-1-carboxylic acid, as catalyzed by 1-aminocyclopropane-1-carboxylic acid oxidase. Bacteria catalyze ethylene production, but via the four-electron oxidation of 2-oxoglutarate to give ethylene in an arginine-dependent reaction. Crystallographic and biochemical studies on the Pseudomonas syringae ethylene-forming enzyme reveal a branched mechanism. In one branch, an apparently typical 2-oxoglutarate oxygenase reaction to give succinate, carbon dioxide, and sometimes pyrroline-5-carboxylate occurs. Alternatively, Grob-type oxidative fragmentation of a 2-oxoglutarate-derived intermediate occurs to give ethylene and carbon dioxide. Crystallographic and quantum chemical studies reveal that fragmentation to give ethylene is promoted by binding of l-arginine in a nonoxidized conformation and of 2-oxoglutarate in an unprecedented high-energy conformation that favors ethylene, relative to succinate formation.

    Organizational Affiliation: 

    Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-oxoglutarate-dependent ethylene/succinate-forming enzyme
A, B, C, D
352Pseudomonas savastanoi pv. phaseolicolaMutation(s): 0 
Gene Names: efe
EC: 1.13.12.19, 1.14.20.7
Find proteins for P32021 (Pseudomonas savastanoi pv. phaseolicola)
Go to UniProtKB:  P32021
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE
Download SDF File 
Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
ARG
Query on ARG
Download SDF File 
Download CCD File 
A, B, C, D
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
OGA
Query on OGA
Download SDF File 
Download CCD File 
A, B, C, D
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.839α = 91.56
b = 79.056β = 93.42
c = 97.859γ = 100.80
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references
  • Version 1.2: 2017-05-10
    Type: Database references