Cytochrome c prime beta from Methylococcus capsulatus (Bath)

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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One fold, two functions: cytochrome P460 and cytochromec'-beta from the methanotrophMethylococcus capsulatus(Bath).

Adams, H.R.Krewson, C.Vardanega, J.E.Fujii, S.Moreno, T.Sambongi, Y.Svistunenko, D.Paps, J.Andrew, C.R.Hough, M.A.

(2019) Chem Sci 10: 3031-3041

  • DOI: https://doi.org/10.1039/c8sc05210g
  • Primary Citation of Related Structures:  
    6HIH, 6HIU

  • PubMed Abstract: 

    Nature is adept at utilising highly similar protein folds to carry out very different functions, yet the mechanisms by which this functional divergence occurs remain poorly characterised. In certain methanotrophic bacteria, two homologous pentacoordinate c-type heme proteins have been identified: a cytochrome P460 (cyt P460) and a cytochrome c '-β (cyt cp-β). Cytochromes P460 are able to convert hydroxylamine to nitrous oxide (N 2 O), a potent greenhouse gas. This reactivity is similar to that of hydroxylamine oxidoreductase (HAO), which is a key enzyme in nitrifying and methanotrophic bacteria. Cyt P460 and HAO both have unusual protein-heme cross-links, formed by a Tyr residue in HAO and a Lys in cyt P460. In contrast, cyts cp-β (the only known cytochromes c ' with a β-sheet fold) lack this crosslink and appears to be optimized for binding non-polar molecules (including NO and CO) without enzymatic conversion. Our bioinformatics analysis supports the proposal that cyt cp-β may have evolved from cyt P460 via a gene duplication event. Using high-resolution X-ray crystallography, UV-visible absorption, electron paramagnetic resonance (EPR) and resonance Raman spectroscopy, we have characterized the overall protein folding and active site structures of cyt cp-β and cyt P460 from the obligate methanotroph, Methylococcus capsulatus (Bath). These proteins display a similar β-sheet protein fold, together with a pattern of changes to the heme pocket regions and localised tertiary structure that have converted a hydroxylamine oxidizing enzyme into a gas-binding protein. Structural comparisons provide insights relevant to enzyme redesign for synthetic enzymology and engineering of gas sensor proteins. We also show the widespread occurrence of cyts cp-β and characterise their phylogeny.

  • Organizational Affiliation

    School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK . Email: mahough@essex.ac.uk.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c
A, B
158Methylococcus capsulatus str. BathMutation(s): 0 
Gene Names: ccpMCA2394
Find proteins for G1UBD5 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore G1UBD5 
Go to UniProtKB:  G1UBD5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1UBD5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEC

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
C34 H34 Fe N4 O4
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
C3 H8 O3
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.96α = 90
b = 105.96β = 90
c = 105.96γ = 90
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references