9EIS | pdb_00009eis

Ethylene forming enzyme in complex with manganese and 2-oxoglutarate from Penicillium digitatum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.286 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.252 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Biochemical, Structural, and Conformational Characterization of a Fungal Ethylene-Forming Enzyme.

Chatterjee, S.Rankin, J.A.Farrugia, M.A.J S Rifayee, S.B.Christov, C.Z.Hu, J.Hausinger, R.P.

(2025) Biochemistry 64: 2054-2067

  • DOI: https://doi.org/10.1021/acs.biochem.5c00038
  • Primary Citation of Related Structures:  
    9EIR, 9EIS

  • PubMed Abstract: 

    The ethylene-forming enzyme (EFE) from the fungus Penicillium digitatum strain Pd1 was heterologously produced in Escherichia coli and its properties were compared to the extensively characterized bacterial enzyme from Pseudomonas savastanoi strain PK2. Both enzymes catalyze four reactions: the conversion of 2-oxoglutarate (2OG) to ethylene and CO 2 , oxidative decarboxylation of 2OG coupled to l-arginine (l-Arg) hydroxylation, uncoupled oxidative decarboxylation of 2OG, and the production of 3-hydroxypropionate (3-HP) from 2OG. The strain Pd1 enzyme exhibited a greater ratio of ethylene production over l-Arg hydroxylation than the PK2 strain EFE. The uncoupled decarboxylation of 2OG and 3-HP production are minor reactions in both cases, but they occur to a greater extent using the fungal enzyme. Additional distinctions of the fungal versus bacterial enzyme are noted in the absorbance maxima and l-Arg dependence of their anaerobic electronic spectra. The structures of the Pd1 EFE apoprotein and the EFE·Mn(II)·2OG complex resembled the corresponding structures of the PK2 enzyme, but notable structural differences were observed in the computationally predicted Pd1 EFE·Fe(II)·2OG·l-Arg complex versus the PK2 EFE·Mn(II)·2OG·l-Arg crystal structure. These studies extend our biochemical understanding and represent the first structural and conformational characterization of a eukaryotic EFE.


  • Organizational Affiliation
    • Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-oxoglutarate-dependent ethylene/succinate-forming enzyme
A, B, C, D
407Penicillium digitatum Pd1Mutation(s): 0 
Gene Names: Pdw03_5776
UniProt
Find proteins for K9GJX7 (Penicillium digitatum (strain Pd1 / CECT 20795))
Explore K9GJX7 
Go to UniProtKB:  K9GJX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9GJX7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKG (Subject of Investigation/LOI)
Query on AKG

Download Ideal Coordinates CCD File 
E [auth A],
I [auth C]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
L [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B],
J [auth C],
M [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth B],
K [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.286 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.159α = 90
b = 117.4β = 90
c = 140.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1904295
National Science Foundation (NSF, United States)United States2203472

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Database references