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: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.8 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: https://doi.org/10.1038/srep35169
  • Primary Citation of Related Structures:  
    5TI9, 5TIA

  • 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 with the substrates L-Trp and O 2 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 O 2 on the C 2 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan 2,3-dioxygenase
A, B, C, D
380Homo sapiensMutation(s): 0 
Gene Names: TDO2TDO
EC: 1.13.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P48775 (Homo sapiens)
Explore P48775 
Go to UniProtKB:  P48775
PHAROS:  P48775
GTEx:  ENSG00000151790 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48775
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
O [auth C],
R [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NFK
Query on NFK

Download Ideal Coordinates CCD File 
P [auth C],
S [auth D]
N'-Formylkynurenine
C11 H12 N2 O4
BYHJHXPTQMMKCA-QMMMGPOBSA-N
TRP
Query on TRP

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
L [auth B]
M [auth B]
Q [auth C]
G [auth A],
H [auth A],
L [auth B],
M [auth B],
Q [auth C],
T [auth D]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
OXY
Query on OXY

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.601α = 90
b = 154.009β = 90
c = 87.801γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50 GM62413
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54 GM074958

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2016-11-09
    Changes: Structure summary
  • Version 1.3: 2016-11-30
    Changes: Structure summary
  • Version 1.4: 2016-12-14
    Changes: Structure summary
  • Version 1.5: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.6: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.7: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.8: 2023-11-15
    Changes: Data collection