4IQ9

Substrate and reaction specificity of Mycobacterium tuberculosis cytochrome P450 CYP121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Substrate and Reaction Specificity of Mycobacterium tuberculosis Cytochrome P450 CYP121: INSIGHTS FROM BIOCHEMICAL STUDIES AND CRYSTAL STRUCTURES.

Fonvielle, M.Le Du, M.H.Lequin, O.Lecoq, A.Jacquet, M.Thai, R.Dubois, S.Grach, G.Gondry, M.Belin, P.

(2013) J Biol Chem 288: 17347-17359

  • DOI: https://doi.org/10.1074/jbc.M112.443853
  • Primary Citation of Related Structures:  
    4ICT, 4IPS, 4IPW, 4IQ7, 4IQ9

  • PubMed Abstract: 

    Cytochrome P450 CYP121 is essential for the viability of Mycobacterium tuberculosis. Studies in vitro show that it can use the cyclodipeptide cyclo(l-Tyr-l-Tyr) (cYY) as a substrate. We report an investigation of the substrate and reaction specificities of CYP121 involving analysis of the interaction between CYP121 and 14 cYY analogues with various modifications of the side chains or the diketopiperazine (DKP) ring. Spectral titration experiments show that CYP121 significantly bound only cyclodipeptides with a conserved DKP ring carrying two aryl side chains in l-configuration. CYP121 did not efficiently or selectively transform any of the cYY analogues tested, indicating a high specificity for cYY. The molecular determinants of this specificity were inferred from both crystal structures of CYP121-analog complexes solved at high resolution and solution NMR spectroscopy of the analogues. Bound cYY or its analogues all displayed a similar set of contacts with CYP121 residues Asn(85), Phe(168), and Trp(182). The propensity of the cYY tyrosyl to point toward Arg(386) was dependent on the presence of the DKP ring that limits the conformational freedom of the ligand. The correct positioning of the hydroxyl of this tyrosyl was essential for conversion of cYY. Thus, the specificity of CYP121 results from both a restricted binding specificity and a fine-tuned P450 substrate relationship. These results document the catalytic mechanism of CYP121 and improve our understanding of its function in vivo. This work contributes to progress toward the design of inhibitors of this essential protein of M. tuberculosis that could be used for antituberculosis therapy.


  • Organizational Affiliation

    Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), iBiTec-S, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette Cedex, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 121395Mycobacterium tuberculosisMutation(s): 0 
Gene Names: cyp121Rv2276MT2336MTCY339.34c
EC: 1.14
UniProt
Find proteins for P9WPP7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPP7 
Go to UniProtKB:  P9WPP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / 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
1GB
Query on 1GB

Download Ideal Coordinates CCD File 
K [auth A](3S,6S)-3-(4-hydroxybenzyl)-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione
C20 H19 N3 O3
ZJDMXAAEAVGGSK-ROUUACIJSA-N
SO4
Query on SO4

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],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
J [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1GB Binding MOAD:  4IQ9 Kd: 3.90e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.647α = 90
b = 77.647β = 90
c = 263.569γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
FFTmodel building
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
FFTphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-08
    Changes: Database references
  • Version 1.2: 2013-07-03
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations