6GII

The crystal structure of Tepidiphilus thermophilus P450 heme domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s.

Tavanti, M., Porter, J.L., Levy, C.W., Gomez Castellanos, J.R., Flitsch, S.L., Turner, N.J.

(2018) Biochem Biophys Res Commun 501: 846-850

  • DOI: 10.1016/j.bbrc.2018.05.014
  • Primary Citation of Related Structures:  
    6GII

  • PubMed Abstract: 

    • The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes ...

    The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes.

    Organizational Affiliation: 

    Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom. Electronic address: nicholas.turner@manchester.ac.uk.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450A479Tepidiphilus thermophilusMutation(s): 0 
Gene Names: Ga0061068_103196
UniProt
Find proteins for A0A0K6ITW2 (Tepidiphilus thermophilus)
Explore A0A0K6ITW2 
Go to UniProtKB:  A0A0K6ITW2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
 B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.292α = 90
b = 74.384β = 90
c = 105.013γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-05-11 
  • Released Date: 2018-05-30 
    • Deposition Author(s): Levy, C.W.
Funding OrganizationLocationGrant Number
European UnionUnited Kingdom613849
European UnionUnited Kingdom635734

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references