Cytochrome P450 XplA heme domain P21212

Experimental Data Snapshot

  • Resolution: 1.49 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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The 1.5-A Structure of Xpla-Heme, an Unusual Cytochrome P450 Heme Domain that Catalyzes Reductive Biotransformation of Royal Demolition Explosive.

Sabbadin, F.Jackson, R.Haider, K.Tampi, G.Turkenburg, J.P.Hart, S.Bruce, N.C.Grogan, G.

(2009) J Biol Chem 284: 28467

  • DOI: https://doi.org/10.1074/jbc.M109.031559
  • Primary Citation of Related Structures:  
    2WIV, 2WIY

  • PubMed Abstract: 

    XplA is a cytochrome P450 of unique structural organization, consisting of a heme-domain that is C-terminally fused to its native flavodoxin redox partner. XplA, along with flavodoxin reductase XplB, has been shown to catalyze the breakdown of the nitramine explosive and pollutant hexahydro-1,3,5-trinitro-1,3,5-triazine (royal demolition explosive) by reductive denitration. The structure of the heme domain of XplA (XplA-heme) has been solved in two crystal forms: as a dimer in space group P2(1) to a resolution of 1.9 A and as a monomer in space group P2(1)2(1)2 to a resolution of 1.5 A, with the ligand imidazole bound at the heme iron. Although it shares the overall fold of cytochromes P450 of known structure, XplA-heme is unusual in that the kinked I-helix that traverses the distal face of the heme is broken by Met-394 and Ala-395 in place of the well conserved Asp/Glu plus Thr/Ser, important in oxidative P450s for the scission of the dioxygen bond prior to substrate oxygenation. The heme environment of XplA-heme is hydrophobic, featuring a cluster of three methionines above the heme, including Met-394. Imidazole was observed bound to the heme iron and is in close proximity to the side chain of Gln-438, which is situated over the distal face of the heme. Imidazole is also hydrogen-bonded to a water molecule that sits in place of the threonine side-chain hydroxyl exemplified by Thr-252 in Cyt-P450cam. Both Gln-438 --> Ala and Ala-395 --> Thr mutants of XplA-heme displayed markedly reduced activity compared with the wild type for royal demolition explosive degradation when combined with surrogate electron donors.

  • Organizational Affiliation

    Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME P450-LIKE PROTEIN XPLA394RhodococcusMutation(s): 0 
Find proteins for Q8GPH7 (Rhodococcus rhodochrous)
Explore Q8GPH7 
Go to UniProtKB:  Q8GPH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GPH7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C34 H32 Fe N4 O4
Query on IMD

Download Ideal Coordinates CCD File 
C3 H5 N2
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.49 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.293α = 90
b = 64.677β = 90
c = 54.048γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata 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: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description