TDO2 (human) — gene review notes

UniProt: P48775 (T23O_HUMAN). Gene: TDO2 (HGNC:11708). 406 aa. Chromosome 4.

Core identity and function

TDO2 encodes tryptophan 2,3-dioxygenase (TDO; EC 1.13.11.11), a heme-dependent
dioxygenase that catalyzes the oxidative cleavage of the pyrrole ring of L-tryptophan,
converting L-tryptophan + O2 to N-formyl-L-kynurenine. This is the first and
rate-limiting, committed step of the kynurenine pathway of tryptophan catabolism, which
routes ~95% of dietary tryptophan and ultimately supplies de novo NAD+ biosynthesis.

• UniProt FUNCTION: "Heme-dependent dioxygenase that catalyzes the oxidative cleavage of
  the L-tryptophan (L-Trp) pyrrole ring and converts L-tryptophan to N-formyl-L-kynurenine.
  Catalyzes the oxidative cleavage of the indole moiety."
  [file:human/TDO2/TDO2-uniprot.txt]
• CATALYTIC ACTIVITY: "L-tryptophan + O2 = N-formyl-L-kynurenine; ... EC=1.13.11.11"
  (Rhea:RHEA:24536). [file:human/TDO2/TDO2-uniprot.txt]
• COFACTOR: "Name=heme ... Note=Binds 1 heme group per subunit." His328 is the axial
  (proximal) heme iron ligand. [file:human/TDO2/TDO2-uniprot.txt]
• PATHWAY: "Amino-acid degradation; L-tryptophan degradation via kynurenine pathway;
  L-kynurenine from L-tryptophan: step 1/2." [file:human/TDO2/TDO2-uniprot.txt]
• SUBUNIT: "Homotetramer. Dimer of dimers." [file:human/TDO2/TDO2-uniprot.txt]

TDO is PMID:27762317; "The majority of dietary Trp (~95%) is metabolized in the liver through this
pathway to produce NAD+" PMID:27762317. TDO is PMID:28285122, contrasting with the immune enzyme IDO1 which has widespread tissue distribution,
less substrate specificity, and inflammation-induced activity PMID:28285122. In mouse
knockout models, TDO was estimated PMID:28285122.

Structure / catalysis

• Crystal structure of human TDO in ternary complex with L-Trp and O2, and binary complex
  with product N-formylkynurenine (NFK): PMID:27762317. Reaction "initiated by a direct
  attack of O2 on the C2 atom of the L-Trp indole ring." Proximal ligand: "the proximal
  His328 ligand coming from the C-terminal region of helix αJ."
• Apo (heme-free) hTDO structure at 2.90 Å; tetramer, active-site architecture conserved;
  mutational studies confirmed eight residues critical for L-Trp oxidation
  [PMID:25066423 abstract]. Key active-site mutants (Y42A, Y45A, F72A, H76A, F140A, R144A,
  S151A, H328A) reduce/abolish activity (UniProt MUTAGEN, ECO:0000269|PubMed:25066423).
• Homotetramer / dimer of dimers confirmed by gel filtration; disease variant Met108Ile
  "is predominately a homotetramer as reported for the native human enzyme" PMID:28285122.
• Exo (non-catalytic) L-Trp binding site ~42 Å from active site regulates cellular stability:
  L-Trp binding to this exo site "retards the degradation of hTDO through the
  ubiquitin-dependent proteasomal pathway" PMID:27762317. This is the molecular basis for
  substrate-induced stabilization / short half-life of TDO.

Localization

Cytosolic enzyme. Reactome: "Cytosolic tryptophan 2,3-dioxygenase (TDO) tetramer catalyzes
the conversion of L-tryptophan and oxygen to formylkynurenine" [Reactome:R-HSA-71188].
Enzyme assayed directly from liver cytosol across species PMID:29959909. GO cytosol annotations: IDA (PMID:29959909, FlyBase),
TAS (Reactome), IEA (orthology). Consistent — cytosol accepted as core CC.

Regulation / physiology

• Hepatic; induced by substrate (tryptophan), by histidine, and by glucocorticoids
  [Reactome:R-HSA-71188 "induced by metabolites such as tryptophan and histidine, and by
  glucocorticoids"]. Comings et al. reported a glucocorticoid-response-like element in the
  TDO2 promoter [PMID:8666386, sequence paper].
• Disease: Hypertryptophanemia (HYPTRP, MIM:600627), autosomal recessive, first human
  case with compound heterozygous TDO2 variants (Met108Ile + a frameshift) established by
  PMID:28285122. Biochemical phenotype (persistent hypertryptophanemia + hyperserotoninemia)
  reported as benign/without significant clinical consequences in that case.

Ensembl-projected IEA BP annotations (rat ortholog P21643)

response to ethanol (GO:0045471), response to cortisol (GO:0051414), response to dexamethasone (GO:0071548), response to nitroglycerin (GO:1904842). These are
electronically transferred from the rat ortholog via Ensembl Compara (GO_REF:0000107,
ECO:0000265). Cortisol/dexamethasone responses are biologically plausible (TDO is a classic
glucocorticoid-inducible hepatic enzyme; see Reactome and the glucocorticoid-response element
in PMID:8666386) — kept as non-core regulatory/stimulus-response terms. response to ethanol
and response to nitroglycerin are narrow rat-specific transcriptional-response observations,
kept as non-core. None are core molecular functions.

Molecular-function / binding IEA annotations to scrutinize

• amino acid binding (GO:0016597, IEA Ensembl from rat): substrate L-Trp is an amino acid;
  this is a generic parent capturing substrate binding. Kept as non-core (the specific
  catalytic MF GO:0004833 already entails L-Trp binding).
• oxygen binding (GO:0019825, in UniProt DR but not in current GOA TSV): O2 is a
  co-substrate; captured by catalytic activity. (Not present as a separate row in the GOA
  TSV under review, so no annotation entry needed.)
• metal ion binding (GO:0046872, IEA InterPro/UniProtKB-KW): TDO binds heme iron; the
  informative term is heme binding (GO:0020037, well supported by IDA). metal ion binding
  is a redundant generic parent — MARK_AS_OVER_ANNOTATED.

Protein-binding IPI annotations (over-annotation)

All protein binding (GO:0005515) IPI rows derive from high-throughput interactome / Y2H /
affinity-capture screens (PMID:16189514, 24722188, 25416956, 25910212, 28514442, 31515488,
32296183, 32814053, 33961781). Partners (AHCYL1, ASMTL, CALR, CDH1, DLST, DPM1, EIF4E, LNX1,
MOB1A/3C, NEK7, NGB, NMNAT1, NR1D1, PICK1, PM20D2, SDCBP/2, ZFYVE26, etc.) are heterogeneous
and do not define a specific characterized molecular function for this cytosolic metabolic
enzyme. Per policy, bare protein binding IPI is MARK_AS_OVER_ANNOTATED (not removed).
identical protein binding (GO:0042802, IPI self) reflects the well-established homotetramer
and is retained as non-core supporting evidence for oligomerization (the informative term is
protein homotetramerization, GO:0051289, IDA).

Core functions (summary)

1. MF: L-tryptophan 2,3-dioxygenase activity (GO:0004833) — heme-dependent; well supported
   by IDA/EXP (PMID:25066423, 27762317, 28285122).
2. MF: heme binding (GO:0020037) — cofactor; IDA (PMID:27762317, 28285122).
3. BP: L-tryptophan catabolic process (GO:0006569) — kynurenine pathway; IDA (PMID:27762317).
   Contributes to 'de novo' NAD+ biosynthesis from L-tryptophan (GO:0034354).
   [GO:0019441 "L-tryptophan catabolic process to L-kynurenine" is OBSOLETE — do not use.]
4. CC: cytosol (GO:0005829) — IDA/TAS.

Action tally rationale

• ACCEPT: catalytic MF (GO:0004833) IDA/EXP/TAS/IBA; heme binding (GO:0020037) IDA/IBA;
  L-tryptophan catabolic process (GO:0006569) IDA/IBA; cytosol (GO:0005829) IDA/TAS;
  protein homotetramerization (GO:0051289) IDA.
• ACCEPT (IEA, correct): GO:0004833 IEA, GO:0006569 IEA, GO:0020037 IEA, cytosol IEA.
• KEEP_AS_NON_CORE: identical protein binding (self/homotetramer); amino acid binding;
  response to cortisol; response to dexamethasone; response to ethanol; response to
  nitroglycerin.
• MARK_AS_OVER_ANNOTATED: metal ion binding (redundant generic parent of heme binding);
  all bare protein binding IPI (high-throughput interactome).