5BV5

Structure of CYP119 with T213A and C317H mutations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural Adaptability Facilitates Histidine Heme Ligation in a Cytochrome P450.

McIntosh, J.A.Heel, T.Buller, A.R.Chio, L.Arnold, F.H.

(2015) J Am Chem Soc 137: 13861-13865

  • DOI: https://doi.org/10.1021/jacs.5b07107
  • Primary Citation of Related Structures:  
    5BV5

  • PubMed Abstract: 

    Almost all known members of the cytochrome P450 (CYP) superfamily conserve a key cysteine residue that coordinates the heme iron. Although mutation of this residue abolishes monooxygenase activity, recent work has shown that mutation to either serine or histidine unlocks non-natural carbene- and nitrene-transfer activities. Here we present the first crystal structure of a histidine-ligated P450. The T213A/C317H variant of the thermostable CYP119 from Sulfolobus acidocaldarius maintains heme iron coordination through the introduced ligand, an interaction that is accompanied by large changes in the overall protein structure. We also find that the axial cysteine C317 may be substituted with any other amino acid without abrogating folding and heme cofactor incorporation. Several of the axial mutants display unusual spectral features, suggesting that they have active sites with unique steric and electronic properties. These novel, highly stable enzyme active sites will be fruitful starting points for investigations of non-natural P450 catalysis and mechanisms.


  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 119A,
B,
C [auth D],
D [auth C]
368Saccharolobus solfataricusMutation(s): 0 
UniProt
Find proteins for Q55080 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore Q55080 
Go to UniProtKB:  Q55080
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ55080
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth D],
L [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PIM
Query on PIM

Download Ideal Coordinates CCD File 
I [auth B],
K [auth D],
M [auth C]
4-PHENYL-1H-IMIDAZOLE
C9 H8 N2
XHLKOHSAWQPOFO-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.486α = 90
b = 137.871β = 101.18
c = 91.779γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1F32GM110851
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1F32GM101792

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Data collection, Derived calculations
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references, Derived calculations