8HKJ | pdb_00008hkj

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 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 645.58 kDa 
  • Atom Count: 41,062 
  • Modeled Residue Count: 4,996 
  • Deposited Residue Count: 5,496 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
EC: 1.14.14.1 (UniProt), 1.6.2.4 (UniProt)
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
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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 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
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

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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
  • Version 1.3: 2024-05-29
    Changes: Data collection