1URO

UROPORPHYRINOGEN DECARBOXYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of human uroporphyrinogen decarboxylase.

Whitby, F.G.Phillips, J.D.Kushner, J.P.Hill, C.P.

(1998) EMBO J. 17: 2463-2471

  • DOI: 10.1093/emboj/17.9.2463

  • PubMed Abstract: 
  • Uroporphyrinogen decarboxylase (URO-D) catalyzes the fifth step in the heme biosynthetic pathway, converting uroporphyrinogen to coproporphyrinogen by decarboxylating the four acetate side chains of the substrate. This activity is essential in all or ...

    Uroporphyrinogen decarboxylase (URO-D) catalyzes the fifth step in the heme biosynthetic pathway, converting uroporphyrinogen to coproporphyrinogen by decarboxylating the four acetate side chains of the substrate. This activity is essential in all organisms, and subnormal activity of URO-D leads to the most common form of porphyria in humans, porphyria cutanea tarda (PCT). We have determined the crystal structure of recombinant human URO-D at 1.60 A resolution. The 40.8 kDa protein is comprised of a single domain containing a (beta/alpha)8-barrel with a deep active site cleft formed by loops at the C-terminal ends of the barrel strands. Many conserved residues cluster at this cleft, including the invariant side chains of Arg37, Arg41 and His339, which probably function in substrate binding, and Asp86, Tyr164 and Ser219, which may function in either binding or catalysis. URO-D is a dimer in solution (Kd = 0.1 microM), and this dimer also appears to be formed in the crystal. Assembly of the dimer juxtaposes the active site clefts of the monomers, suggesting a functionally important interaction between the catalytic centers.


    Organizational Affiliation

    Department of Biochemistry, University of Utah School of Medicine, 50 N.Medical Drive, Salt Lake City, UT 84132, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (UROPORPHYRINOGEN DECARBOXYLASE)
A
367Homo sapiensGene Names: UROD
EC: 4.1.1.37
Find proteins for P06132 (Homo sapiens)
Go to Gene View: UROD
Go to UniProtKB:  P06132
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.000α = 90.00
b = 103.000β = 90.00
c = 73.700γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance