4L36

Crystal structure of the cytochrome P450 enzyme TxtE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural Insights into the Mechanism for Recognizing Substrate of the Cytochrome P450 Enzyme TxtE.

Yu, F.Li, M.J.Xu, C.Y.Wang, Z.J.Zhou, H.Yang, M.Chen, Y.X.Tang, L.He, J.H.

(2013) PLoS One 8: e81526-e81526

  • DOI: 10.1371/journal.pone.0081526
  • Primary Citation of Related Structures:  
    4L36

  • PubMed Abstract: 
  • Thaxtomins, a family of phytotoxins produced by Streptomyces spp., can cause dramatic plant cell hypertrophy and seedling stunting. Thaxtomin A is the dominant form from Streptomyces scabies and has demonstrated herbicidal action. TxtE, a cytochrome P450 enzyme from Streptomyces scabies 87 ...

    Thaxtomins, a family of phytotoxins produced by Streptomyces spp., can cause dramatic plant cell hypertrophy and seedling stunting. Thaxtomin A is the dominant form from Streptomyces scabies and has demonstrated herbicidal action. TxtE, a cytochrome P450 enzyme from Streptomyces scabies 87.22, catalyzes direct nitration of the indolyl moiety of L-tryptophan to L-4-nitrotryptophan using nitric oxide, dioxygen and NADPH. The crystal structure of TxtE was determined at 2.1 Å resolution and described in this work. A clearly defined substrate access channel is observed and can be classified as channel 2a, which is common in bacteria cytochrome P450 enzymes. A continuous hydrogen bond chain from the active site to the external solvent is observed. Compared with other cytochrome P450 enzymes, TxtE shows a unique proton transfer pathway which crosses the helix I distortion. Polar contacts of Arg59, Tyr89, Asn293, Thr296, and Glu394 with L-tryptophan are seen using molecular docking analysis, which are potentially important for substrate recognition and binding. After mutating Arg59, Asn293, Thr296 or Glu394 to leucine, the substrate binding ability of TxtE was lost or decreased significantly. Based on the docking and mutation results, a possible mechanism for substrate recognition and binding is proposed.


    Organizational Affiliation

    Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative P450-like proteinA, B426Streptomyces scabiei 87.22Mutation(s): 0 
Gene Names: SCAB_31831
UniProt
Find proteins for C9ZDC6 (Streptomyces scabiei (strain 87.22))
Explore C9ZDC6 
Go to UniProtKB:  C9ZDC6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEB
Query on HEB

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]HEME B/C
C34 H34 Fe N4 O4
NEGHHAJBRZGUAY-ICENSXKYDL
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], G [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.316α = 77.76
b = 52.595β = 82.17
c = 88.245γ = 68.36
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release