3G5H

Crystallographic analysis of cytochrome P450 cyp121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification and structural basis of the reaction catalyzed by CYP121, an essential cytochrome P450 in Mycobacterium tuberculosis.

Belin, P.Le Du, M.H.Fielding, A.Lequin, O.Jacquet, M.Charbonnier, J.B.Lecoq, A.Thai, R.Courcon, M.Masson, C.Dugave, C.Genet, R.Pernodet, J.L.Gondry, M.

(2009) Proc.Natl.Acad.Sci.USA 106: 7426-7431

  • DOI: 10.1073/pnas.0812191106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The gene encoding the cytochrome P450 CYP121 is essential for Mycobacterium tuberculosis. However, the CYP121 catalytic activity remains unknown. Here, we show that the cyclodipeptide cyclo(l-Tyr-l-Tyr) (cYY) binds to CYP121, and is efficiently conve ...

    The gene encoding the cytochrome P450 CYP121 is essential for Mycobacterium tuberculosis. However, the CYP121 catalytic activity remains unknown. Here, we show that the cyclodipeptide cyclo(l-Tyr-l-Tyr) (cYY) binds to CYP121, and is efficiently converted into a single major product in a CYP121 activity assay containing spinach ferredoxin and ferredoxin reductase. NMR spectroscopy analysis of the reaction product shows that CYP121 catalyzes the formation of an intramolecular C-C bond between 2 tyrosyl carbon atoms of cYY resulting in a novel chemical entity. The X-ray structure of cYY-bound CYP121, solved at high resolution (1.4 A), reveals one cYY molecule with full occupancy in the large active site cavity. One cYY tyrosyl approaches the heme and establishes a specific H-bonding network with Ser-237, Gln-385, Arg-386, and 3 water molecules, including the sixth iron ligand. These observations are consistent with low temperature EPR spectra of cYY-bound CYP121 showing a change in the heme environment with the persistence of the sixth heme iron ligand. As the carbon atoms involved in the final C-C coupling are located 5.4 A apart according to the CYP121-cYY complex crystal structure, we propose that C-C coupling is concomitant with substrate tyrosyl movements. This study provides insight into the catalytic activity, mechanism, and biological function of CYP121. Also, it provides clues for rational design of putative CYP121 substrate-based antimycobacterial agents.


    Organizational Affiliation

    Service d'Ingénierie Moléculaire des Protéines, Biologie Structurale et Mécanismes, Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, F-91191 Gif-sur-Yvette, France. pascal.belin@cea.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 121
A
396Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: cyp121
EC: 1.14.19.70
Find proteins for P9WPP7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WPP7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YTT
Query on YTT

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Download CCD File 
A
(3S,6S)-3,6-bis(4-hydroxybenzyl)piperazine-2,5-dione
cyclo(tyrosyl-tyrosyl), Cyclo(tyr-tyr)
C18 H18 N2 O4
NGPCLOGFGKJCBP-HOTGVXAUSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.151 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.690α = 90.00
b = 77.690β = 90.00
c = 262.737γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
FFTmodel building
FFTphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-12-09
    Type: Database references