8X8F | pdb_00008x8f

Crystal structure of lipoxygenase from Enhygromyxa salina


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.254 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Discovery and Molecular Characterization of a Novel 9 S -Lipoxygenase from Enhygromyxa salina for Fatty Acid Biotransformations.

Kim, J.W.Yoon, J.H.Lee, J.Cha, H.J.Seo, P.W.Lee, T.E.Bornscheuer, U.T.Oh, D.K.Park, J.B.Kim, J.S.

(2024) J Agric Food Chem 72: 26263-26273

  • DOI: https://doi.org/10.1021/acs.jafc.4c01258
  • Primary Citation Related Structures: 
    8X8F

  • PubMed Abstract: 

    Iron-dependent lipoxygenases (LOXs) are involved in the synthesis of oxylipins from polyunsaturated fatty acids. However, they are usually difficult to overexpress in functional form in microbial cell factories. Moreover, 9-LOXs, generating 9-hydroperoxy fatty acids from C18 polyunsaturated fatty acids, have rarely been found from microbial sources. Here, we discovered a novel 9 S -LOX in the marine myxobacterium Enhygromyxa salina (Es-9 S -LOX). The recombinant enzyme produced in Escherichia coli exhibited remarkable activity in the dioxygenation of linoleic acid (LA, 1 ), α-linolenic acid, γ-linolenic acid, and arachidonic acid specifically at the C9 position to yield the product with ( S )-configuration at catalytic efficiency of 3.94, 1.42, 1.38, and 0.69 μM -1 ·s -1 , respectively. The elucidated X-ray crystal structure of Es-9 S -LOX reveals a long and narrow hydrophobic pocket that allows the substrate to be near the metal ion and the oxygen tunnel. The enzyme was successfully used in a chemoenzymatic reaction to generate a hydroxy fatty acid from LA. Our study thus contributes to the valorization of renewable polyunsaturated fatty acids into a variety of fatty acid derivatives, including hydroxy fatty acids.


  • Organizational Affiliation
    • Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 852.45 kDa 
  • Atom Count: 56,680 
  • Modeled Residue Count: 7,239 
  • Deposited Residue Count: 7,800 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arachidonate 15-lipoxygenase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
650Enhygromyxa salinaMutation(s): 0 
Gene Names: DB30_08017
UniProt
Find proteins for A0A0C2CV93 (Enhygromyxa salina)
Explore A0A0C2CV93 
Go to UniProtKB:  A0A0C2CV93
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0C2CV93
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
(Subject of Investigation/LOI)

Query on CD



Download:Ideal Coordinates CCD File
AA [auth D]
AB [auth K]
BA [auth D]
BB [auth K]
CA [auth E]
AA [auth D],
AB [auth K],
BA [auth D],
BB [auth K],
CA [auth E],
CB [auth K],
DA [auth E],
DB [auth K],
EA [auth E],
EB [auth L],
FA [auth E],
FB [auth L],
GA [auth F],
GB [auth L],
HA [auth F],
HB [auth L],
IA [auth F],
JA [auth F],
KA [auth G],
LA [auth G],
M [auth A],
MA [auth G],
N [auth A],
NA [auth G],
O [auth A],
OA [auth H],
P [auth A],
PA [auth H],
Q [auth B],
QA [auth H],
R [auth B],
RA [auth H],
S [auth B],
SA [auth I],
T [auth B],
TA [auth I],
U [auth C],
UA [auth I],
V [auth C],
VA [auth I],
W [auth C],
WA [auth J],
X [auth C],
XA [auth J],
Y [auth D],
YA [auth J],
Z [auth D],
ZA [auth J]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.254 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.726α = 90
b = 248.59β = 119.86
c = 164.089γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Database references
  • Version 1.2: 2026-03-04
    Changes: Refinement description