9CJG | pdb_00009cjg

P450-G9 from Actinokineospora terrae, a non-canonical, serine-ligated cytochrome P450 in the ligand-free, closed conformation

• PDB DOI: https://doi.org/10.2210/pdb9CJG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Actinokineospora terrae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-06 Released: 2025-03-12 
• Deposition Author(s): Ireland, K.A., Davis, K.M.
• Funding Organization(s): National Institutes of Health/John E. Fogarty International Center (NIH/FIC), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.242 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: in silico

Literature

Non-Canonical Cytochrome P450 Enzymes in Nature.

Nguy, A.K.L., Ireland, K.A., Kayrouz, C.M., Caceres, J.C., Greene, B.L., Davis, K.M., Seyedsayamdost, M.R.

(2024) bioRxiv 

• PubMed: 39763895 
• DOI: https://doi.org/10.1101/2024.12.22.630014
• Primary Citation of Related Structures:  
  9CJG


• PubMed Abstract: 
  

  Cytochrome P450s (CYPs) are a superfamily of thiolate-ligated heme metalloenzymes principally responsible for the hydroxylation of unactivated C-H bonds. The lower-axial cysteine is an obligatory and universally conserved residue for the CYP enzyme class. Herein, we challenge this paradigm by systematically identifying non-canonical CYPs (ncCYPs) that do not harbor a cysteine ligand. Our bioinformatic search reveals 20 distinct ncCYP families with diverse ligands encoded in microbial genomes. We characterize a native serine-ligated CYP with a high-spin ferric resting state. Its crystal structure clearly shows a typical CYP fold and a serine alkoxide as a lower axial heme ligand. In addition, we report the discovery and characterization of the first native selenocysteine-ligated CYP in nature. Our findings radically expand the CYP metalloenzyme family.

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Organizational Affiliation: 
• Department of Chemistry, Princeton University, Princeton, NJ, USA.
These authors contributed equally.
Department of Chemistry, Emory University, Atlanta, GA, USA.
Interdepartmental Program in Quantitative Biosciences, University of California Santa Barbara, Santa Barbara, CA, USA.
Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA.
Department of Molecular Biology, Princeton University, Princeton, NJ, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 90.33 kDa 
• Atom Count: 6,282 
• Modeled Residue Count: 772 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450-G9	A, B	411	Actinokineospora terrae	Mutation(s): 0  Gene Names: SAMN04487818_101238 EC: 1.14
UniProt
Find proteins for A0A1H9KM06 (Actinokineospora terrae) Explore A0A1H9KM06  Go to UniProtKB:  A0A1H9KM06

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
1BO	E [auth A], F [auth A]	1-BUTANOL C4 H10 O LRHPLDYGYMQRHN-UHFFFAOYSA-N
FMT	D [auth A], G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.242 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.13	α = 90
b = 59.65	β = 90
c = 233.8	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Ireland, K.A., Davis, K.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)	United States	R35-GM147557
National Science Foundation (NSF, United States)	United States	1937971

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release