1UWK

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and Action of Urocanase

Kessler, D.Retey, J.Schulz, G.E.

(2004) J.Mol.Biol. 342: 183

  • DOI: 10.1016/j.jmb.2004.07.028
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UROCANATE HYDRATASE
A, B
557Pseudomonas putidaMutation(s): 2 
Gene Names: hutU
EC: 4.2.1.49
Find proteins for P25080 (Pseudomonas putida)
Go to UniProtKB:  P25080
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URO
Query on URO

Download SDF File 
Download CCD File 
A, B
(2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID
C6 H6 N2 O2
LOIYMIARKYCTBW-OWOJBTEDSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.429α = 90.00
b = 71.618β = 98.75
c = 129.158γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SHELXL-97refinement
XSCALEdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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