9TK7 | pdb_00009tk7

Cryogenic temperature structure of urocanate reductase in complex with imidazole propionate and sulfate

PDB DOI: https://doi.org/10.2210/pdb9TK7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Shewanella oneidensis MR-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-12-08 Released: 2026-05-20
Deposition Author(s): Aggarwal, S., Gurav, N., Oksanen, E., Lindkvist-Petersson, K., Venskutonyte, R.
Funding Organization(s): Swedish Research Council, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.139 (Depositor), 0.139 (DCC)
R-Value Work:
0.113 (Depositor), 0.114 (DCC)
R-Value Observed:
0.114 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural insights into urocanate reductase using room-temperature X-ray crystallography.

Aggarwal, S., Gurav, N., Oksanen, E., Lindkvist-Petersson, K., Venskutonyte, R.

(2026) Acta Crystallogr D Struct Biol

PubMed: 42083916 Search on PubMed
DOI: https://doi.org/10.1107/S2059798326003360
Primary Citation Related Structures:
9TK1, 9TK3, 9TK5, 9TK6, 9TK7, 9TK8

PubMed Abstract:
Urocanate reductase (UrdA) is a bacterial enzyme that converts urocanic acid to imidazole propionate. Its catalytic residue Arg411 undergoes a large conformational change in the substrate-bound versus product-bound states. In contrast to previously studied cryo-conditions, the room-temperature X-ray data of UrdA presented here show that the occupancy distribution of Arg411 is affected by crystal cryocooling. We further provide evidence that a phosphate ion stabilizes the substrate complex and can bias the conformation of Arg411. Both room-temperature and cryogenic X-ray datasets were essential to elucidate the dynamic nature of the UrdA active site, highlighting the importance of collecting data at both temperatures, as each may reveal distinct conformational states.

Organizational Affiliation

European Spallation Source ERIC (ESS), 221 00 Lund, Sweden.

Macromolecule Content

Total Structure Weight: 51.77 kDa
Atom Count: 4,172
Modeled Residue Count: 454
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urocanate reductase	A	460	Shewanella oneidensis MR-1	Mutation(s): 0 Gene Names: urdA, SO_4620 EC: 1.3.99.33
UniProt
Find proteins for Q8CVD0 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8CVD0 Go to UniProtKB: Q8CVD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8CVD0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MWQ (Subject of Investigation/LOI) Query on MWQ Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	3-(1~{H}-imidazol-5-yl)propanoic acid C₆ H₈ N₂ O₂ ZCKYOWGFRHAZIQ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]