5TI9

Crystal structure of human TDO in complex with Trp and dioxygen, Northeast Structural Genomics Consortium Target HR6161


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase.

Lewis-Ballester, A.Forouhar, F.Kim, S.M.Lew, S.Wang, Y.Karkashon, S.Seetharaman, J.Batabyal, D.Chiang, B.Y.Hussain, M.Correia, M.A.Yeh, S.R.Tong, L.

(2016) Sci Rep 6: 35169-35169

  • DOI: 10.1038/srep35169
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) play a central role in tryptophan metabolism and are involved in many cellular and disease processes. Here we report the crystal structure of human TDO (hTDO) in a ternary complex ...

    Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) play a central role in tryptophan metabolism and are involved in many cellular and disease processes. Here we report the crystal structure of human TDO (hTDO) in a ternary complex with the substrates L-Trp and O2 and in a binary complex with the product N-formylkynurenine (NFK), defining for the first time the binding modes of both substrates and the product of this enzyme. The structure indicates that the dioxygenation reaction is initiated by a direct attack of O2 on the C2 atom of the L-Trp indole ring. The structure also reveals an exo binding site for L-Trp, located ~42 Å from the active site and formed by residues conserved among tryptophan-auxotrophic TDOs. Biochemical and cellular studies indicate that Trp binding at this exo site does not affect enzyme catalysis but instead it retards the degradation of hTDO through the ubiquitin-dependent proteasomal pathway. This exo site may therefore provide a novel L-Trp-mediated regulation mechanism for cellular degradation of hTDO, which may have important implications in human diseases.


    Organizational Affiliation

    Department of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophan 2,3-dioxygenase
A, B, C, D
380Homo sapiensMutation(s): 0 
Gene Names: TDO2 (TDO)
EC: 1.13.11.11
Find proteins for P48775 (Homo sapiens)
Go to Gene View: TDO2
Go to UniProtKB:  P48775
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, B
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
TRP
Query on TRP

Download SDF File 
Download CCD File 
A, B, C, D
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
NFK
Query on NFK

Download SDF File 
Download CCD File 
C, D
N'-Formylkynurenine
(2S)-2-amino-4-[2-(formylamino)phenyl]-4-oxobutanoic acid
C11 H12 N2 O4
BYHJHXPTQMMKCA-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 143.601α = 90.00
b = 154.009β = 90.00
c = 87.801γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP50 GM62413
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU54 GM074958

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Type: Database references
  • Version 1.2: 2016-11-09
    Type: Structure summary
  • Version 1.3: 2016-11-30
    Type: Structure summary
  • Version 1.4: 2016-12-14
    Type: Structure summary
  • Version 1.5: 2017-09-27
    Type: Author supporting evidence