22NW | pdb_000022nw

ethylene forming enzyme in complex with 2-oxoglutarate

• PDB DOI: https://doi.org/10.2210/pdb22NW/pdb

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


• Deposited: 2026-01-17 Released: 2026-09-09 
• Deposition Author(s): Zhou, J.H., Wang, M.Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.196 (Depositor) 
• R-Value Work: 
  0.174 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: in silico

wwPDB Validation

Currently 22NW does not have a validation slider image.

Literature

Structure-guided surface engineering to improve the catalytic activity of ethylene-forming enzyme.

Wang, M., Shen, Z., Wu, L., Huang, W., Zhou, J., Gu, Y.

(2026) Eng Microbiol 6: 100276-100276

• PubMed: 42238545 
• DOI: https://doi.org/10.1016/j.engmic.2026.100276
• Primary Citation Related Structures: 
  22NW, 22PE


• PubMed Abstract: 
  

  The ethylene-forming enzyme (EFE) is a member of the mononuclear non-heme Fe(II)- and 2-oxoglutarate-dependent oxygenase superfamily, which can oxidize 2-oxoglutarate to form ethylene in an arginine-dependent reaction. While significant enzyme engineering efforts have targeted the active site and surface of EFE, to date, no variant with substantially improved activity has been reported. To enhance catalytic activity and broaden the application potential of EFE, this study developed a surface engineering strategy based on structural analysis and potentially new l-Arg binding information. The resulting variant, E213T, exhibited a 1.5-fold increase in catalytic activity and a 2.4-fold elevation in k _{cat, l-Arg} . Molecular dynamics simulations further revealed that this amino acid substitution reduced the affinity of the surface l-Arg binding site and altered the accessibility of ligands to the catalytic center. Our study provides a new perspective on the distal sites and functional relationships in protein engineering of EFE.

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Organizational Affiliation: 
• Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
State Key Laboratory of Microbial Technology, Nanjing Normal University, Nanjing 210023, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.67 kDa 
• Atom Count: 2,974 
• Modeled Residue Count: 342 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate-dependent ethylene/succinate-forming enzyme	A	349	Pseudomonas savastanoi pv. phaseolicola	Mutation(s): 0  Gene Names: efe EC: 1.13.12.19 (PDB Primary Data), 1.14.20.7 (PDB Primary Data)
UniProt
Find proteins for P32021 (Pseudomonas savastanoi pv. phaseolicola) Explore P32021  Go to UniProtKB:  P32021

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG( Subject of Investigation/LOI)	D [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE2( Subject of Investigation/LOI)	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.196 (Depositor) 
• R-Value Work:  0.174 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.252	α = 90
b = 97.766	β = 90
c = 97.918	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Currently 22NW does not have a validation slider image.

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-09 
Deposition Author(s): Zhou, J.H., Wang, M.Y.

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Funding Organization	Location	Grant Number
Not funded	China	--

Revision History  

• Version 1.0: 2026-09-09
  Type: Initial release