Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.56 kDa 
• Atom Count: 3060 
• Modelled Residue Count: 357 
• Deposited Residue Count: 384 
• Unique protein chains: 1

7TTQ

P450 (OxyA) from kistamicin biosynthesis, imidazole complex

• PDB DOI: 10.2210/pdb7TTQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Actinomadura parvosata subsp. kistnae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-02-01 Released: 2022-05-11 
• Deposition Author(s): Greule, A., Izore, T., Cryle, M.J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC), German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.203 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

The Cytochrome P450 OxyA from the Kistamicin Biosynthesis Cyclization Cascade is Highly Sensitive to Oxidative Damage.

Greule, A., Izore, T., Machell, D., Hansen, M.H., Schoppet, M., De Voss, J.J., Charkoudian, L.K., Schittenhelm, R.B., Harmer, J.R., Cryle, M.J.

(2022) Front Chem 10: 868240-868240

• PubMed: 35464232 
• DOI: 10.3389/fchem.2022.868240
• Primary Citation of Related Structures:  
  7TTA, 7TTB, 7TTO, 7TTP, 7TTQ


• PubMed Abstract: 
  

Cytochrome P450 enzymes (P450s) are a superfamily of monooxygenases that utilize a cysteine thiolate-ligated heme moiety to perform a wide range of demanding oxidative transformations. Given the oxidative power of the active intermediate formed within P450s during their active cycle, it is remarkable that these enzymes can avoid auto-oxidation and retain the axial cysteine ligand in the deprotonated-and thus highly acidic-thiolate form. While little is known about the process of heme incorporation during P450 folding, there is an overwhelming preference for one heme orientation within the P450 active site. Indeed, very few structures to date contain an alternate heme orientation, of which two are OxyA homologs from glycopeptide antibiotic (GPA) biosynthesis. Given the apparent preference for the unusual heme orientation shown by OxyA enzymes, we investigated the OxyA homolog from kistamicin biosynthesis (OxyA _kis ), which is an atypical GPA. We determined that OxyA _kis is highly sensitive to oxidative damage by peroxide, with both UV and EPR measurements showing rapid bleaching of the heme signal. We determined the structure of OxyA _kis and found a mixed population of heme orientations present in this enzyme. Our analysis further revealed the possible modification of the heme moiety, which was only present in samples where the alternate heme orientation was present in the protein. These results suggest that the typical heme orientation in cytochrome P450s can help prevent potential damage to the heme-and hence deactivation of the enzyme-during P450 catalysis. It also suggests that some P450 enzymes involved in GPA biosynthesis may be especially prone to oxidative damage due to the heme orientation found in their active sites.

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Organizational Affiliation: 

ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome P450 hydroxylase	A	384	Actinomadura parvosata subsp. kistnae	Mutation(s): 0  Gene Names: KIS93_04812 EC: 1
UniProt
Find proteins for A0A2P9IBF7 (Actinomadura parvosata subsp. kistnae) Explore A0A2P9IBF7  Go to UniProtKB:  A0A2P9IBF7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	B [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.203 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.659	α = 90
b = 69.659	β = 90
c = 132.354	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2022-02-01 
• Released Date: 2022-05-11 
Deposition Author(s): Greule, A., Izore, T., Cryle, M.J.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1140619
Australian Research Council (ARC)	Australia	DP170102220
German Research Foundation (DFG)	Germany	CR 392/1-1

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release