Q8PDA8 (T23O_XANCP) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Tryptophan 2,3-dioxygenase
Short name=TDO
EC=1.13.11.11

Alternative name(s):
Tryptamin 2,3-dioxygenase
Tryptophan oxygenase
Short name=TO
Short name=TRPO
Tryptophan pyrrolase
Tryptophanase

Gene names

Name:	kynA
Ordered Locus Names:	XCC0432

Organism

Xanthomonas campestris pv. campestris

Taxonomic identifier

340 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Xanthomonadales › Xanthomonadaceae › Xanthomonas

Protein attributes

Sequence length	298 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the oxidative cleavage of the L-tryptophan (L-Trp) pyrrole ring. Ref.2 Ref.3
Catalytic activity	L-tryptophan + O2 = N-formyl-L-kynurenine. Ref.2 Ref.3
Cofactor	Binds 2 heme groups per tetramer.
Enzyme regulation	Weakly inhibited by D-tryptophan. Ref.2
Pathway	Amino-acid degradation; L-tryptophan degradation via kynurenine pathway; L-kynurenine from L-tryptophan: step 1/2.
Subunit structure	Homotetramer. Ref.2 Ref.3
Sequence similarities	Belongs to the tryptophan 2,3-dioxygenase family.
Biophysicochemical properties	Kinetic parameters: KM=114 µM for L-tryptophan Ref.2 Ref.3 KM=100 µM for 5-fluoro-D/L-tryptophan KM=186 µM for 6-fluoro-D/L-tryptophan KM=357 µM for 5-methyl-D/L-tryptophan KM=975 µM for 6-methyl-D/L-tryptophan KM=119 µM for O2

Ontologies

Keywords
Biological process	Tryptophan catabolism
Ligand	Heme Iron Metal-binding
Molecular function	Dioxygenase Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	protein homotetramerization Inferred from direct assay Ref.3. Source: UniProtKB tryptophan catabolic process to kynurenine Inferred from direct assay Ref.3. Source: UniProtKB
Molecular function	heme binding Inferred from direct assay Ref.3. Source: UniProtKB tryptophan 2,3-dioxygenase activity Inferred from direct assay Ref.3. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 298

298

Tryptophan 2,3-dioxygenase

PRO_0000360143

Regions

Region

24 – 28

5

Substrate binding

Region

51 – 55

5

Substrate binding

Sites

Metal binding

240

1

Iron (heme axial ligand)

Binding site

113

1

Substrate

Binding site

117

1

Substrate

Binding site

124

1

Heme

Binding site

254

1

Substrate

Experimental info

Mutagenesis

55

1

H → A: Decrease in catalytic efficiency using L-tryptophan, 5-fluoro-D/L-tryptophan, 6-fluoro-D/L-tryptophan, 5-methyl-D/L-tryptophan and 6-methyl-D/L-tryptophan as substrate. Ref.2 Ref.3

Mutagenesis

55

1

H → S: Decrease in catalytic efficiency using L-tryptophan, 5-fluoro-D/L-tryptophan, 6-fluoro-D/L-tryptophan, 5-methyl-D/L-tryptophan and 6-methyl-D/L-tryptophan as substrate. Ref.2 Ref.3

Secondary structure

1

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298

Helix Strand Turn

Details...

Helix

30 – 34

5

Helix

48 – 77

30

Helix

81 – 100

20

Helix

102 – 105

4

Helix

110 – 113

4

Helix

117 – 119

3

Helix

129 – 137

9

Helix

143 – 146

4

Turn

148 – 151

4

Helix

157 – 163

7

Helix

168 – 178

11

Helix

185 – 188

4

Helix

200 – 202

3

Helix

203 – 211

9

Turn

213 – 216

4

Helix

217 – 247

31

Helix

263 – 266

4

Helix

273 – 277

5

Helix

278 – 280

3

Sequences

	Sequence		Length	Mass (Da)
	Q8PDA8 [UniParc]. Last modified October 1, 2002. Version 1. Checksum: 544600380EDD4A3D	FASTA	298	34,617
	10 20 30 40 50 60 MPVDKNLRDL EPGIHTDLEG RLTYGGYLRL DQLLSAQQPL SEPAHHDEML FIIQHQTSEL 70 80 90 100 110 120 WLKLLAHELR AAIVHLQRDE VWQCRKVLAR SKQVLRQLTE QWSVLETLTP SEYMGFRDVL 130 140 150 160 170 180 GPSSGFQSLQ YRYIEFLLGN KNPQMLQVFA YDPAGQARLR EVLEAPSLYE EFLRYLARFG 190 200 210 220 230 240 HAIPQQYQAR DWTAAHVADD TLRPVFERIY ENTDRYWREY SLCEDLVDVE TQFQLWRFRH 250 260 270 280 290 MRTVMRVIGF KRGTGGSSGV GFLQQALALT FFPELFDVRT SVGVDNRPPQ GSADAGKR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Comparison of the genomes of two Xanthomonas pathogens with differing host specificities." da Silva A.C.R., Ferro J.A., Reinach F.C., Farah C.S., Furlan L.R., Quaggio R.B., Monteiro-Vitorello C.B., Van Sluys M.A., Almeida N.F. Jr., Alves L.M.C., do Amaral A.M., Bertolini M.C., Camargo L.E.A., Camarotte G., Cannavan F., Cardozo J., Chambergo F., Ciapina L.P. , Cicarelli R.M.B., Coutinho L.L., Cursino-Santos J.R., El-Dorry H., Faria J.B., Ferreira A.J.S., Ferreira R.C.C., Ferro M.I.T., Formighieri E.F., Franco M.C., Greggio C.C., Gruber A., Katsuyama A.M., Kishi L.T., Leite R.P., Lemos E.G.M., Lemos M.V.F., Locali E.C., Machado M.A., Madeira A.M.B.N., Martinez-Rossi N.M., Martins E.C., Meidanis J., Menck C.F.M., Miyaki C.Y., Moon D.H., Moreira L.M., Novo M.T.M., Okura V.K., Oliveira M.C., Oliveira V.R., Pereira H.A., Rossi A., Sena J.A.D., Silva C., de Souza R.F., Spinola L.A.F., Takita M.A., Tamura R.E., Teixeira E.C., Tezza R.I.D., Trindade dos Santos M., Truffi D., Tsai S.M., White F.F., Setubal J.C., Kitajima J.P. Nature 417:459-463(2002) [PubMed: 12024217] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 33913 / NCPPB 528 / LMG 568.
[2]	"Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase." Forouhar F., Anderson J.L.R., Mowat C.G., Vorobiev S.M., Hussain A., Abashidze M., Bruckmann C., Thackray S.J., Seetharaman J., Tucker T., Xiao R., Ma L.-C., Zhao L., Acton T.B., Montelione G.T., Chapman S.K., Tong L. Proc. Natl. Acad. Sci. U.S.A. 104:473-478(2007) [PubMed: 17197414] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH L-TRYPTOPHAN AND HEME, FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, KINETIC PARAMETERS, HOMOTETRAMERIZATION, MUTAGENESIS OF HIS-55.
[3]	"Histidine 55 of tryptophan 2,3-dioxygenase is not an active site base but regulates catalysis by controlling substrate binding." Thackray S.J., Bruckmann C., Anderson J.L.R., Campbell L.P., Xiao R., Zhao L., Mowat C.G., Forouhar F., Tong L., Chapman S.K. Biochemistry 47:10677-10684(2008) [PubMed: 18783250] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF MUTANTS ALA-55 AND SER-55 IN COMPLEX WITH L-TRYPTOPHAN AND HEME, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, HOMOTETRAMERIZATION, MUTAGENESIS OF HIS-55.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE008922 Genomic DNA. Translation: AAM39750.1.

RefSeq

NP_635826.1. NC_003902.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1YW0	X-ray	2.70	A/B/C/D	23-298	[»]
2NW7	X-ray	2.70	A/B/C/D	1-298	[»]
2NW8	X-ray	1.60	A/B	1-298	[»]
2NW9	X-ray	1.80	A/B	1-298	[»]
3BK9	X-ray	2.15	A/B/C/D/E/F/G/H	1-298	[»]
3E08	X-ray	1.90	A/B/C/D/E/F/G/H	1-298	[»]

ProteinModelPortal

Q8PDA8.

SMR

Q8PDA8. Positions 19-284.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1000901.

GenomeReviews

Gene locus XCC0432 in contig AE008922_GR.

KEGG

xcc:XCC0432.

PATRIC

24071477. VBIXanCam115730_0475.

Phylogenomic databases

HOGENOM

HBG647485.

OMA

QYREIEF.

ProtClustDB

CLSK539120.

Enzyme and pathway databases

BioCyc

XCAM190485:XCC0432-MONOMER.

Family and domain databases

InterPro

IPR004981. Trp_2_3_dOase.
[Graphical view]

KO

K00453.

PANTHER

PTHR10138. Trp_2_3_dOase. 1 hit.

Pfam

PF03301. Trp_dioxygenase. 2 hits.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

T23O_XANCP

Accession

Primary (citable) accession number: Q8PDA8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 20, 2009
Last sequence update:	October 1, 2002
Last modified:	January 25, 2012
This is version 53 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program