7P46

Crystal Structure of Xanthomonas campestris Tryptophan 2,3-dioxygenase (TDO)

PDB DOI: https://doi.org/10.2210/pdb7P46/pdb

Classification: OXIDOREDUCTASE
Organism(s): Xanthomonas campestris pv. campestris str. ATCC 33913
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-09 Released: 2021-10-06
Deposition Author(s): Kwon, H., Basran, J., Booth, E.S., Campbell, L.P., Thackray, S.J., Moody, P.C.E., Mowat, C.G., Raven, E.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.185
R-Value Work: 0.149
R-Value Observed: 0.151

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Binding of l-kynurenine to X. campestris tryptophan 2,3-dioxygenase.

Basran, J., Booth, E.S., Campbell, L.P., Thackray, S.J., Jesani, M.H., Clayden, J., Moody, P.C.E., Mowat, C.G., Kwon, H., Raven, E.L.

(2021) J Inorg Biochem 225: 111604-111604

PubMed: 34571402 Search on PubMed
DOI: https://doi.org/10.1016/j.jinorgbio.2021.111604
Primary Citation of Related Structures:
7P46

PubMed Abstract:
The kynurenine pathway is the major route of tryptophan metabolism. The first step of this pathway is catalysed by one of two heme-dependent dioxygenase enzymes - tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) - leading initially to the formation of N-formylkynurenine (NFK). In this paper, we present a crystal structure of a bacterial TDO from X. campestris in complex with l-kynurenine, the hydrolysed product of NFK. l-kynurenine is bound at the active site in a similar location to the substrate (l-Trp). Hydrogen bonding interactions with Arg117 and the heme 7-propionate anchor the l-kynurenine molecule into the pocket. A mechanism for the hydrolysis of NFK in the active site is presented.

Organizational Affiliation

Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK.

Macromolecule Content

Total Structure Weight: 273.22 kDa
Atom Count: 21,574
Modelled Residue Count: 2,235
Deposited Residue Count: 2,256
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan 2,3-dioxygenase	A, B, C, D, E A, B, C, D, E, F, G, H	282	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 0 Gene Names: kynA, XCC0432 EC: 1.13.11.11
UniProt
Find proteins for Q8PDA8 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8PDA8 Go to UniProtKB: Q8PDA8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8PDA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain IA [auth E] SDF format, chain QA [auth G] SDF format, chain Y [auth C] SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain LA [auth F] SDF format, chain S [auth B] SDF format, chain TA [auth H] MOL2 format, chain IA [auth E] MOL2 format, chain QA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth H] mmCIF format, chain IA [auth E] mmCIF format, chain QA [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth H]	EA [auth D] I [auth A] IA [auth E] LA [auth F] QA [auth G] EA [auth D], I [auth A], IA [auth E], LA [auth F], QA [auth G], S [auth B], TA [auth H], Y [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain EA [auth D] Focus chain I [auth A] Focus chain IA [auth E] Focus chain LA [auth F] Focus chain QA [auth G] Focus chain S [auth B] Focus chain TA [auth H] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain I [auth A] Focus chain IA [auth E] Focus chain LA [auth F] Focus chain QA [auth G] Focus chain S [auth B] Focus chain TA [auth H] Focus chain Y [auth C]
KYN Query on KYN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain NA [auth F] SDF format, chain RA [auth G] SDF format, chain U [auth B] SDF format, chain VA [auth H] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain RA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth H] mmCIF format, chain AA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain RA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth H]	AA [auth C] GA [auth D] JA [auth E] K [auth A] NA [auth F] AA [auth C], GA [auth D], JA [auth E], K [auth A], NA [auth F], RA [auth G], U [auth B], VA [auth H]	(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid C₁₀ H₁₂ N₂ O₃ YGPSJZOEDVAXAB-QMMMGPOBSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain JA [auth E] Focus chain K [auth A] Focus chain NA [auth F] Focus chain RA [auth G] Focus chain U [auth B] Focus chain VA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain JA [auth E] Focus chain K [auth A] Focus chain NA [auth F] Focus chain RA [auth G] Focus chain U [auth B] Focus chain VA [auth H]
TRP Query on TRP Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain L [auth A] SDF format, chain V [auth B] SDF format, chain BA [auth C] SDF format, chain KA [auth E] SDF format, chain OA [auth F] SDF format, chain SA [auth G] SDF format, chain WA [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain V [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain KA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain SA [auth G] MOL2 format, chain WA [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain V [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain KA [auth E] mmCIF format, chain OA [auth F] mmCIF format, chain SA [auth G] mmCIF format, chain WA [auth H]	BA [auth C] HA [auth D] KA [auth E] L [auth A] OA [auth F] BA [auth C], HA [auth D], KA [auth E], L [auth A], OA [auth F], SA [auth G], V [auth B], WA [auth H]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain BA [auth C] Focus chain HA [auth D] Focus chain KA [auth E] Focus chain L [auth A] Focus chain OA [auth F] Focus chain SA [auth G] Focus chain V [auth B] Focus chain WA [auth H] Interactions & Density Focus chain BA [auth C] Focus chain HA [auth D] Focus chain KA [auth E] Focus chain L [auth A] Focus chain OA [auth F] Focus chain SA [auth G] Focus chain V [auth B] Focus chain WA [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain R [auth A] SDF format, chain X [auth B] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth F] SDF format, chain Q [auth A] SDF format, chain W [auth B] SDF format, chain XA [auth H] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth A] MOL2 format, chain X [auth B] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth H] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth A] mmCIF format, chain X [auth B] mmCIF format, chain YA [auth H] mmCIF format, chain ZA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain W [auth B] mmCIF format, chain XA [auth H]	CA [auth C] DA [auth C] M [auth A] N [auth A] O [auth A] CA [auth C], DA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], PA [auth F], Q [auth A], R [auth A], W [auth B], X [auth B], XA [auth H], YA [auth H], ZA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain R [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth H] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain R [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth H] Focus chain YA [auth H] Focus chain ZA [auth H]
CYN Query on CYN Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain J [auth A] SDF format, chain MA [auth F] SDF format, chain T [auth B] SDF format, chain UA [auth H] SDF format, chain Z [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain Z [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain Z [auth C]	FA [auth D] J [auth A] MA [auth F] T [auth B] UA [auth H] FA [auth D], J [auth A], MA [auth F], T [auth B], UA [auth H], Z [auth C]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain J [auth A] Focus chain MA [auth F] Focus chain T [auth B] Focus chain UA [auth H] Focus chain Z [auth C] Interactions & Density Focus chain FA [auth D] Focus chain J [auth A] Focus chain MA [auth F] Focus chain T [auth B] Focus chain UA [auth H] Focus chain Z [auth C]