6AMG

cyt P460 of Nitrosomonas sp. AL212


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

The Eponymous Cofactors in Cytochrome P460s from Ammonia-Oxidizing Bacteria Are Iron Porphyrinoids Whose Macrocycles Are Dibasic.

Smith, M.A.Lancaster, K.M.

(2018) Biochemistry 57: 334-343

  • DOI: https://doi.org/10.1021/acs.biochem.7b00921
  • Primary Citation of Related Structures:  
    6AMG

  • PubMed Abstract: 

    The enzymes hydroxylamine oxidoreductase and cytochrome (cyt) P460 contain related unconventional "heme P460" cofactors. These cofactors are unusual in their inclusion of nonstandard cross-links between amino acid side chains and the heme macrocycle. Mutagenesis studies performed on the Nitrosomonas europaea cyt P460 that remove its lysine-heme cross-link show that the cross-link is key to defining the spectroscopic properties and kinetic competence of the enzyme. However, exactly how this cross-link confers these features remains unclear. Here we report the 1.45 Å crystal structure of cyt P460 from Nitrosomonas sp. AL212 and conclude that the cross-link does not lead to a change in hybridization of the heme carbon participating in the cross-link but rather enforces structural distortions to the macrocycle away from planarity. Time-dependent density functional theory coupled to experimental structural and spectroscopic analysis suggest that this geometric distortion is sufficient to define the spectroscopic properties of the heme P460 cofactor and provide clues toward establishing a relationship between heme P460 electronic structure and function.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P460
A, B
196Nitrosomonas sp. AL212Mutation(s): 0 
Gene Names: NAL212_0896
UniProt
Find proteins for F9ZFJ0 (Nitrosomonas sp. AL212)
Explore F9ZFJ0 
Go to UniProtKB:  F9ZFJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF9ZFJ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.267α = 90
b = 80.138β = 90
c = 108.962γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 1.2: 2018-02-07
    Changes: Database references
  • Version 1.3: 2020-02-26
    Changes: Data collection
  • Version 2.0: 2021-03-10
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description