9JQM | pdb_00009jqm

X-ray structure of cytochrome P450 OleT from Lacicoccus alkaliphilus in complex with icosanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 
    0.230 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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Literature

Unique structural features define the decarboxylation activity of a CYP152 fatty acid decarboxylase from Lacicoccus alkaliphilus.

Phaisan, S.Phintha, A.Trisrivirat, D.Lawan, N.Sucharitakul, J.Charoenpol, A.Watthaisong, P.Tanaka, H.Kurisu, G.Chaiyen, P.

(2025) J Biological Chem 301: 110397-110397

  • DOI: https://doi.org/10.1016/j.jbc.2025.110397
  • Primary Citation of Related Structures:  
    9JQM

  • PubMed Abstract: 

    Cytochrome P450 CYP152s catalyze decarboxylation of fatty acids to generate terminal alkenes, valuable compounds for various industries. Here, we identified, overexpressed, and characterized a new CYP152 enzyme from Lacicoccus alkaliphilus (OleT LA ) and compared its biophysical and biochemical properties with the well-studied OleT JE from Jeotgalicoccus sp. 8456. Improved expression protocols gave the highest yields of CYP152 holoenzymes reported to date. OleT LA exhibits twice the catalytic turnover number of OleT JE when using hexadecanoic acid and H 2 O 2 as substrates in 10% (v/v) ethanol (EtOH). The X-ray structure of OleT LA in complex with icosanoic acid revealed a unique flipped heme and a substrate tunnel configuration which are different than those of other CYP152 decarboxylases. Molecular dynamics simulations revealed that in the presence of EtOH, OleT LA displays structural dynamics which maintain structural interactions better than those of OleT JE . As I178 in OleT LA (equivalent to L176 in OleT JE ) shows close interactions with its substrate during simulations, I178L of OleT LA and L176I of OleT JE variants were constructed and investigated for their activities. While L176I in OleT JE caused a significant loss of activity, I178L of OleT LA had activities that were equivalent to or greater than those of the wild-type enzyme, suggesting that overall scaffold of OleT LA is more amenable to mutation than OleT JE . Stopped-flow investigations of OleT LA reactions indicated that EtOH increases the rate constant of Compound I formation. We also identified a new redox partner system, ferredoxin and ferredoxin reductase that can function as effective electron donors for both in vitro and in vivo systems of CYP152s.


  • Organizational Affiliation

    School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty-acid peroxygenaseA [auth B],
B [auth A]
432Lacicoccus alkaliphilus DSM 16010Mutation(s): 0 
Gene Names: SAMN02745189_00740
UniProt
Find proteins for A0A1M7CBV6 (Lacicoccus alkaliphilus DSM 16010)
Explore A0A1M7CBV6 
Go to UniProtKB:  A0A1M7CBV6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1M7CBV6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth B],
H [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
DCR (Subject of Investigation/LOI)
Query on DCR

Download Ideal Coordinates CCD File 
D [auth B],
I [auth A]
icosanoic acid
C20 H40 O2
VKOBVWXKNCXXDE-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth B]
F [auth B]
G [auth B]
J [auth A]
K [auth A]
E [auth B],
F [auth B],
G [auth B],
J [auth A],
K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free:  0.230 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.799α = 90
b = 188.859β = 90
c = 198.313γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Vidyasirimedhi Institute of Science and Technology (VISTEC)Thailand--
Program Management Unit for Human Resources & Institutional Development (PMU-B) Research and InnovationThailandB05F640089
Thailand Science Research and InnovationThailandFRB670026/0457
KasikornBank Public Company LimitedThailand--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release