BRENDA - Enzyme Database show
show all sequences of 1.13.11.11

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.; Sci. Rep. 6, 35169 (2016)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
recombinant expression of full-length His6-tagged hTDO protein in human liver HepG2 cell culture
Homo sapiens
Crystallization (Commentary)
Crystallization
Organism
purified enzyme in a ternary complex with the substrates L-Trp and O2 and in a binary complex with the product N-formylkynurenine, under-oil microbatch method under anaerobic conditions, mixing of 0.003 ml of 45 mg/ml protein in 50 mM Tris, pH 8.0, containing 150 mM NaCl and 10 mM L-Trp, and reduced with 2-fold molar excess of sodium dithionite, with 0.003-0.006 ml of precipitannt solution containing 50 mM sodium citrate, pH 5.6, 5% w/v PEG 3350, and 2% w/v Tacsimate, pH 5.0, X-ray diffraction structure determination and analysis at 2.5 A and 2.44 A resolution, respectively. Crystals of the Trp-bound binary complex are soaked in an O2-saturated precipitant solution supplemented with 20% v/v ethylene glycol at room temperature
Homo sapiens
Engineering
Amino acid exchange
Commentary
Organism
Y175G
site-directed mutagenesis, the mutation leads to a 6fold slower multiple turnover velocity. In addition, pre-incubation of the Y175G mutant with 8 mM NFK retards the formation of the ternary complex by about 100fold and impedes Trp binding
Homo sapiens
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
stopped-flow kinetics
Homo sapiens
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
heme with Fe2+ coordinated by 4 N-atoms, overview
Homo sapiens
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-tryptophan + O2
Homo sapiens
-
N-formyl-L-kynurenine
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Homo sapiens
P48775
-
-
Reaction
Reaction
Commentary
Organism
L-tryptophan + O2 = N-formyl-L-kynurenine
the dioxygenation reaction is initiated by a direct attack of O2 on the C2 atom of the L-Trp indole ring, catalytic mechanism, overview. Exo binding site for L-Trp, located about 42 A from the active site and formed by residues conserved among tryptophan-auxotrophic TDOs. 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
Homo sapiens
Source Tissue
Source Tissue
Commentary
Organism
Textmining
Hep-G2 cell
-
Homo sapiens
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-tryptophan + O2
-
743821
Homo sapiens
N-formyl-L-kynurenine
-
-
-
?
additional information
substrate recognition and binding structures, overview. The EG segment in hTDO plays a critical role in promoting NFK release, thereby allowing Trp binding during multiple turnover
743821
Homo sapiens
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
tetramer
-
Homo sapiens
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Homo sapiens
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Homo sapiens
Cofactor
Cofactor
Commentary
Organism
Structure
heme
with Fe2+ coordinated by 4 N-atoms, overview
Homo sapiens
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant expression of full-length His6-tagged hTDO protein in human liver HepG2 cell culture
Homo sapiens
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
heme
with Fe2+ coordinated by 4 N-atoms, overview
Homo sapiens
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified enzyme in a ternary complex with the substrates L-Trp and O2 and in a binary complex with the product N-formylkynurenine, under-oil microbatch method under anaerobic conditions, mixing of 0.003 ml of 45 mg/ml protein in 50 mM Tris, pH 8.0, containing 150 mM NaCl and 10 mM L-Trp, and reduced with 2-fold molar excess of sodium dithionite, with 0.003-0.006 ml of precipitannt solution containing 50 mM sodium citrate, pH 5.6, 5% w/v PEG 3350, and 2% w/v Tacsimate, pH 5.0, X-ray diffraction structure determination and analysis at 2.5 A and 2.44 A resolution, respectively. Crystals of the Trp-bound binary complex are soaked in an O2-saturated precipitant solution supplemented with 20% v/v ethylene glycol at room temperature
Homo sapiens
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
Y175G
site-directed mutagenesis, the mutation leads to a 6fold slower multiple turnover velocity. In addition, pre-incubation of the Y175G mutant with 8 mM NFK retards the formation of the ternary complex by about 100fold and impedes Trp binding
Homo sapiens
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
stopped-flow kinetics
Homo sapiens
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
heme with Fe2+ coordinated by 4 N-atoms, overview
Homo sapiens
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-tryptophan + O2
Homo sapiens
-
N-formyl-L-kynurenine
-
-
?
Source Tissue (protein specific)
Source Tissue
Commentary
Organism
Textmining
Hep-G2 cell
-
Homo sapiens
-
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-tryptophan + O2
-
743821
Homo sapiens
N-formyl-L-kynurenine
-
-
-
?
additional information
substrate recognition and binding structures, overview. The EG segment in hTDO plays a critical role in promoting NFK release, thereby allowing Trp binding during multiple turnover
743821
Homo sapiens
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
tetramer
-
Homo sapiens
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Homo sapiens
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Homo sapiens
General Information
General Information
Commentary
Organism
additional information
the exo site regulates hTDO cellular stability
Homo sapiens
General Information (protein specific)
General Information
Commentary
Organism
additional information
the exo site regulates hTDO cellular stability
Homo sapiens
Other publictions for EC 1.13.11.11
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
743153
Nienhaus
Substrate binding primes huma ...
Homo sapiens
J. Phys. Chem. B
121
7412-7420
2017
-
-
-
-
-
-
-
1
-
1
-
1
-
2
-
-
-
1
-
-
-
-
2
-
-
-
-
-
1
-
-
1
-
-
-
-
-
-
1
-
-
-
-
-
-
1
-
1
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
1
-
-
-
-
2
2
-
-
-
743358
Gonzalez Esquivel
Kynurenine pathway metabolite ...
Homo sapiens, Mus musculus, Xanthomonas campestris pv. campestris, Xanthomonas campestris pv. campestris ATCC 33913
Neuropharmacology
112
331-345
2017
2
-
-
-
-
-
3
2
-
-
-
-
-
7
-
-
-
-
-
29
-
-
4
2
-
-
-
-
-
-
-
3
-
-
-
2
-
-
5
-
-
-
-
3
-
3
-
-
-
-
-
-
-
-
-
31
-
-
4
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
741938
Basran
Analysis of reaction intermed ...
Homo sapiens, Xanthomonas campestris pv. campestris, Xanthomonas campestris pv. campestris ATCC 33913
Biochemistry
55
6743-6750
2016
-
-
2
-
-
-
-
2
-
2
-
3
-
4
-
-
2
-
-
-
-
-
12
-
2
-
-
-
2
-
-
2
-
-
-
-
-
2
2
-
-
-
-
-
-
2
-
2
-
3
-
-
-
2
-
-
-
-
12
-
2
-
-
-
2
-
-
-
-
4
4
-
-
-
742986
Pantouris
Insights into the mechanism o ...
Homo sapiens
J. Enzyme Inhib. Med. Chem.
31
70-78
2016
-
1
-
-
-
-
2
-
1
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
2
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
743821
Lewis-Ballester
Molecular basis for catalysis ...
Homo sapiens
Sci. Rep.
6
35169
2016
-
-
1
1
1
-
-
1
-
1
-
1
-
2
-
-
-
1
-
1
-
-
2
1
1
-
-
-
1
-
-
1
-
-
-
-
-
1
1
1
1
-
-
-
-
1
-
1
-
1
-
-
-
-
-
1
-
-
2
1
1
-
-
-
1
-
-
-
-
1
1
-
-
-
743005
Yuasa
Efficient tryptophan-cataboli ...
Branchiostoma floridae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Monosiga brevicollis, Nematostella vectensis, no activity in Brugia malayi, no activity in Saccharomyces cerevisiae, no activity in Schistosoma mansoni, Rattus norvegicus, Strongylocentrotus purpuratus
J. Exp. Zool. B
324
128-140
2015
-
-
8
-
-
-
-
11
-
-
-
8
-
14
-
-
-
-
-
-
-
-
8
-
8
-
-
-
3
-
-
1
-
-
-
-
-
8
1
-
-
-
-
-
-
11
-
-
-
8
-
-
-
-
-
-
-
-
8
-
8
-
-
-
3
-
-
-
-
8
8
-
-
-
743064
Wu
Identification of substituted ...
Homo sapiens
J. Med. Chem.
58
7807-7819
2015
-
1
1
-
-
-
21
-
-
-
-
1
-
1
-
-
1
-
-
2
-
-
1
-
1
-
-
-
1
-
-
1
-
-
20
-
1
1
1
-
-
-
20
21
-
-
-
-
-
1
-
-
-
1
-
2
-
-
1
-
1
-
-
-
1
-
-
-
-
3
3
-
-
-
742114
Maeta
Contributions of tryptophan 2 ...
Mus musculus, Mus musculus C57BL/6
Biosci. Biotechnol. Biochem.
78
878-881
2014
-
-
-
-
1
-
-
-
-
-
-
6
-
3
-
-
-
-
-
1
-
-
8
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
6
-
-
-
-
-
1
-
-
8
-
-
-
-
-
-
-
-
-
-
3
3
-
-
-
743760
Meng
Structural and functional ana ...
Homo sapiens
Proteins
82
3210-3216
2014
-
-
1
1
9
-
-
8
-
-
-
1
-
2
-
-
1
-
-
1
-
-
3
3
1
-
-
7
1
-
-
1
-
-
-
-
-
1
1
1
9
-
-
-
-
8
-
-
-
1
-
-
-
1
-
1
-
-
3
3
1
-
-
7
1
-
-
-
-
2
2
-
-
-