8HKJ

Crystal structure of the CYP102A5 haem Domain isolated from Bacillus cereus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Investigating the applicability of the CYP102A1-decoy-molecule system to other members of the CYP102A subfamily.

Stanfield, J.K.Onoda, H.Ariyasu, S.Kasai, C.Burfoot, E.M.Sugimoto, H.Shoji, O.

(2023) J Inorg Biochem 245: 112235-112235

  • DOI: https://doi.org/10.1016/j.jinorgbio.2023.112235
  • Primary Citation of Related Structures:  
    8HKJ

  • PubMed Abstract: 

    Cytochrome P450 enzymes (CYPs) have attracted much promise as biocatalysts in a push for cleaner and more environmentally friendly catalytic systems. However, changing the substrate specificity of CYPs, such as CYP102A1, can be a challenging task, requiring laborious mutagenesis. An alternative approach is the use of decoy molecules that "trick" the enzyme into becoming active by impersonating the native substrate. Whilst the decoy molecule system has been extensively developed for CYP102A1, its general applicability for other CYP102-family enzymes has yet to be shown. Herein, we demonstrate that decoy molecules can "trick" CYP102A5 and A7 into becoming active and hydroxylating non-native substrates. Furthermore, significant differences in decoy molecule selectivity as well as decoy molecule binding were observed. The X-ray crystal structure of the CYP102A5 haem domain was solved at 2.8 Å, delivering insight into a potential substate-binding site that differs significantly from CYP102A1.


  • Organizational Affiliation

    Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional cytochrome P450/NADPH--P450 reductase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
458Bacillus cereusMutation(s): 0 
Gene Names: BKK64_01385
UniProt
Find proteins for Q81BF4 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711))
Explore Q81BF4 
Go to UniProtKB:  Q81BF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81BF4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth I]
EA [auth J]
GA [auth K]
IA [auth L]
AA [auth H],
CA [auth I],
EA [auth J],
GA [auth K],
IA [auth L],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
V [auth E],
X [auth F],
Y [auth G]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PLM
Query on PLM

Download Ideal Coordinates CCD File 
BA [auth H]
DA [auth I]
FA [auth J]
HA [auth K]
JA [auth L]
BA [auth H],
DA [auth I],
FA [auth J],
HA [auth K],
JA [auth L],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
U [auth D],
W [auth E],
Z [auth G]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.62α = 86.66
b = 126.06β = 79.47
c = 141.44γ = 84.97
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan21H04704
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan22H05129
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan22H05119
Japan Science and TechnologyJapanJPMJAX22B5

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Derived calculations
  • Version 1.2: 2023-08-02
    Changes: Database references