9IY1 | pdb_00009iy1

P450 BS beta mutant F46A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.240 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Unexpected Activities of CYP152 Peroxygenases towards Non-carboxylic Substrates Reveal Novel Substrate Recognition Mechanism and Catalytic Versatility.

Jiang, Y.Gong, P.Li, Z.Li, Z.Li, Y.Wang, B.Huang, H.Peng, W.Gao, X.Li, S.

(2025) Angew Chem Int Ed Engl : e202506614-e202506614

  • DOI: https://doi.org/10.1002/anie.202506614
  • Primary Citation of Related Structures:  
    9IY1

  • PubMed Abstract: 

    Exploring and exploiting the catalytic promiscuity of enzymes is a central topic and captivating challenge in enzymology. CYP152 peroxygenases are attractive biocatalysts for diverse reactions under mild conditions using H2O2 as cofactor. However, their substrate scope is limited by a carboxyl group required for substrate assisted acid-base catalysis, following the well-accepted principle that heme-dependent H2O2-utilizing enzymes employ a carboxyl group within their active sites to facilitate H2O2 activation. Herein, we reveal for the first time that several CYP152 family members can directly degrade various aromatic pollutants without any carboxyl group, exhibiting novel aromatic hydroxylation and dehalogenation activities. Through crystal structure analysis, isotope tracing experiments, and QM/MM calculations, we elucidate that the phenolic hydroxyl group activated by electron-withdrawing substituent(s) functionally replaces the carboxyl group, forming hydrogen bonds with the conserved arginine leading to Compound I formation. The oxygen atom of the newly formed hydroxyl group originates from water, bypassing the conventional oxygen rebound step. These findings provide first insights into the mechanisms of P450 peroxygenases towards non-carboxylic substrates, expanding our knowledge of biological C-H activation and C-halogen bond cleavage beyond canonical P450 reactions. This discovery holds immense potential for harnessing these enzymes in innovative strategies for industrial biocatalysis and environmental remediation.


  • Organizational Affiliation

    Shandong University, State Key Laboratory of Microbial Technology, CHINA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty-acid peroxygenase
A, B, C, D, E
A, B, C, D, E, F
416Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: cypCCYP152A1BSU02100
EC: 1.11.2.4
UniProt
Find proteins for O31440 (Bacillus subtilis (strain 168))
Explore O31440 
Go to UniProtKB:  O31440
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31440
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
AB [auth F]
G [auth A]
JA [auth D]
Q [auth B]
UA [auth E]
AB [auth F],
G [auth A],
JA [auth D],
Q [auth B],
UA [auth E],
Y [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
BB [auth F]
H [auth A]
KA [auth D]
R [auth B]
VA [auth E]
BB [auth F],
H [auth A],
KA [auth D],
R [auth B],
VA [auth E],
Z [auth C]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CA [auth C]
CB [auth F]
EB [auth F]
HA [auth C]
IA [auth C]
CA [auth C],
CB [auth F],
EB [auth F],
HA [auth C],
IA [auth C],
IB [auth F],
NA [auth D],
QA [auth D],
S [auth B],
V [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth C]
FA [auth C]
KB [auth F]
LB [auth F]
MB [auth F]
DA [auth C],
FA [auth C],
KB [auth F],
LB [auth F],
MB [auth F],
NB [auth F],
P [auth A],
RA [auth D],
SA [auth D],
TA [auth D],
W [auth B],
X [auth B],
ZA [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
DB [auth F]
EA [auth C]
FB [auth F]
AA [auth C],
BA [auth C],
DB [auth F],
EA [auth C],
FB [auth F],
GA [auth C],
GB [auth F],
HB [auth F],
I [auth A],
J [auth A],
JB [auth F],
K [auth A],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
O [auth A],
OA [auth D],
PA [auth D],
T [auth B],
U [auth B],
WA [auth E],
XA [auth E],
YA [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.240 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.42α = 90
b = 190.114β = 90
c = 226.571γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release