Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 123.12 kDa 
• Atom Count: 9437 
• Modelled Residue Count: 1107 
• Deposited Residue Count: 1114 
• Unique protein chains: 1

1UWK

The High Resolution Structure of Urocanate Hydratase from Pseudomonas putida in complex with urocanate

• PDB DOI: 10.2210/pdb1UWK/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-02-05 Released: 2004-08-19 
• Deposition Author(s): Kessler, D., Retey, J., Schulz, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.179 
• R-Value Observed: 0.140 

Literature

Structure and Action of Urocanase

Kessler, D., Retey, J., Schulz, G.E.

(2004) J Mol Biol 342: 183

• PubMed: 15313616 
• DOI: 10.1016/j.jmb.2004.07.028
• Primary Citation of Related Structures:  
  1UWK, 1UWL, 1W1U


• PubMed Abstract: 
  

Urocanase (EC 4.2.1.49) from Pseudomonas putida was crystallized after removing one of the seven free thiol groups. The crystal structure was solved by multiwavelength anomalous diffraction (MAD) using a seleno-methionine derivative and then refined at 1.14 A resolution. The enzyme is a symmetric homodimer of 2 x 557 amino acid residues with tightly bound NAD+ cofactors. Each subunit consists of a typical NAD-binding domain inserted into a larger core domain that forms the dimer interface. The core domain has a novel chain fold and accommodates the substrate urocanate in a surface depression. The NAD domain sits like a lid on the core domain depression and points with the nicotinamide group to the substrate. Substrate, nicotinamide and five water molecules are completely sequestered in a cavity. Most likely, one of these water molecules hydrates the substrate during catalysis. This cavity has to open for substrate passage, which probably means lifting the NAD domain. The observed atomic arrangement at the active center gives rise to a detailed proposal for the catalytic mechanism that is consistent with published chemical data. As expected, the variability of the residues involved is low, as derived from a family of 58 proteins annotated as urocanases in the data banks. However, one well-embedded member of this family showed a significant deviation at the active center indicating an incorrect annotation.

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Organizational Affiliation: 

Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, 79104 Freiburg im Breisgau, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UROCANATE HYDRATASE	A, B	557	Pseudomonas putida	Mutation(s): 2  Gene Names: hutU EC: 4.2.1.49
UniProt
Find proteins for P25080 (Pseudomonas putida) Explore P25080  Go to UniProtKB:  P25080

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
URO	D [auth A], F [auth B]	(2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID C6 H6 N2 O2 LOIYMIARKYCTBW-OWOJBTEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.179 
• R-Value Observed: 0.140 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.429	α = 90
b = 71.618	β = 98.75
c = 129.158	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XSCALE	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-05 
• Released Date: 2004-08-19 
Deposition Author(s): Kessler, D., Retey, J., Schulz, G.E.

Revision History  

• Version 1.0: 2004-08-19
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-22
  Changes: Data collection, Other, Refinement description