8GAR

Nitrosomonas europaea Cytochrome P460 Arg44Ala

• PDB DOI: https://doi.org/10.2210/pdb8GAR/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Nitrosomonas europaea
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-02-23 Released: 2023-07-05 
• Deposition Author(s): Bollmeyer, M.M., Lancaster, K.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.201 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Cytochrome P460 Cofactor Maturation Proceeds via Peroxide-Dependent Post-translational Modification.

Bollmeyer, M.M., Coleman, R.E., Majer, S.H., Ferrao, S.D., Lancaster, K.M.

(2023) J Am Chem Soc 145: 14404-14416

• PubMed: 37338957 
• DOI: https://doi.org/10.1021/jacs.3c03608
• Primary Citation of Related Structures:  
  8GAR


• PubMed Abstract: 
  

  Cytochrome P460s are heme enzymes that oxidize hydroxylamine to nitrous oxide. They bear specialized "heme P460" cofactors that are cross-linked to their host polypeptides by a post-translationally modified lysine residue. Wild-type N. europaea cytochrome P460 may be isolated as a cross-link-deficient proenzyme following anaerobic overexpression in E. coli . When treated with peroxide, this proenzyme undergoes maturation to active enzyme with spectroscopic and catalytic properties that match wild-type cyt P460. This maturation reactivity requires no chaperones─it is intrinsic to the protein. This behavior extends to the broader cytochrome c' _β superfamily. Accumulated data reveal key contributions from the secondary coordination sphere that enable selective, complete maturation. Spectroscopic data support the intermediacy of a ferryl species along the maturation pathway.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, 162 Sciences Drive, Ithaca, New York 14853, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.91 kDa 
• Atom Count: 1,388 
• Modelled Residue Count: 153 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P460	A	196	Nitrosomonas europaea	Mutation(s): 1  Gene Names: cyp
UniProt
Find proteins for Q50927 (Nitrosomonas europaea) Explore Q50927  Go to UniProtKB:  Q50927

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC (Subject of Investigation/LOI)	B [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.201 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.111	α = 90
b = 53.111	β = 90
c = 125.894	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Bollmeyer, M.M., Lancaster, K.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM124908

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-07-12
  Changes: Database references