5LUN | pdb_00005lun

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

• PDB DOI: https://doi.org/10.2210/pdb5LUN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas savastanoi pv. phaseolicola
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-09 Released: 2017-04-19 
• Deposition Author(s): McDonough, M.A., Zhang, Z., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 
  0.185 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

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

• PubMed: 28420789 
• DOI: https://doi.org/10.1073/pnas.1617760114
• Primary Citation Related Structures: 
  5LSQ, 5LUN, 5MOF


• 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, 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.

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Organizational Affiliation: 
• Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom.
Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom [e-mail] [e-mail].

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: 160.32 kDa 
• Atom Count: 13,304 
• Modeled Residue Count: 1,358 
• Deposited Residue Count: 1,408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate-dependent ethylene/succinate-forming enzyme	A, B, C, D	352	Pseudomonas savastanoi pv. phaseolicola	Mutation(s): 0  Gene Names: efe EC: 1.13.12.19 (PDB Primary Data), 1.14.11.34 (PDB Primary Data), 1.14.20.7 (UniProt)
UniProt
Find proteins for P32021 (Pseudomonas savastanoi pv. phaseolicola) Explore P32021  Go to UniProtKB:  P32021

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	G [auth A], K [auth B], P [auth C], S [auth D]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
OGA	F [auth A], J [auth B], O [auth C], R [auth D]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
GOL	H [auth A], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	E [auth A], I [auth B], N [auth C], Q [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free:  0.185 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.839	α = 91.56
b = 79.056	β = 93.42
c = 97.859	γ = 100.8

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): McDonough, M.A., Zhang, Z., Schofield, C.J.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-05-03
  Changes: Database references
• Version 1.2: 2017-05-10
  Changes: Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description