2Q71

Uroporphyrinogen Decarboxylase G168R single mutant enzyme in complex with coproporphyrinogen-III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Two Novel Uropophyrinogen Decarboxylase (URO-D) Mutations Causing Hepatoerythropoietic Porphyria (HEP)

Phillips, J.D.Whitby, F.G.Stadtmueller, B.M.Edwards, C.Q.Hill, C.P.Kushner, J.P.

(2007) Transl.Res. 149: 85-91

  • DOI: 10.1016/j.trsl.2006.08.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hepatoerythropoietic porphyria (HEP) is a rare form of porphyria in humans. The disorder is caused by homozygosity or compound heterozygosity for mutations of the uroporphyrinogen decarboxylase (URO-D) gene. Subnormal URO-D activity results in accumu ...

    Hepatoerythropoietic porphyria (HEP) is a rare form of porphyria in humans. The disorder is caused by homozygosity or compound heterozygosity for mutations of the uroporphyrinogen decarboxylase (URO-D) gene. Subnormal URO-D activity results in accumulation of uroporphyrin in the liver, which ultimately mediates the photosensitivity that clinically characterizes HEP. Two previously undescribed URO-D mutations found in a 2-year-old Caucasian boy with HEP, a maternal nonsense mutation (Gln71Stop), and a paternal missense mutation (Gly168Arg) are reported here. Recombinant Gly168Arg URO-D retained 65% of wild-type URO-D activity and studies in Epstein-Barr Virus (EBV)-transformed lymphoblasts indicated that protein levels are reduced, suggesting that the mutant protein might be subjected to accelerated turnover. The crystal structure of Gly168Arg was determined both as the apo-enzyme and with the reaction product bound. These studies revealed little distortion of the active site, but a loop containing residues 167-172 was displaced, possibly indicating small changes in the catalytic geometry or in substrate binding or increased accessibility to a cellular proteolytic pathway. A second pregnancy occurred in this family, and in utero genotyping revealed a fetus heterozygous for the maternal nonsense mutation (URO-D genotype WT/Gln71Stop). A healthy infant was born with no clinical evidence of porphyria.


    Organizational Affiliation

    Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA. john.phillips@hsc.utah.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uroporphyrinogen decarboxylase
A
356Homo sapiensMutation(s): 1 
Gene 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
CP3
Query on CP3

Download SDF File 
Download CCD File 
A
COPROPORPHYRINOGEN III
C36 H44 N4 O8
NIUVHXTXUXOFEB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.162 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.037α = 90.00
b = 103.037β = 90.00
c = 71.865γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
REFMACphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-03-12
    Type: Non-polymer description
  • Version 1.4: 2017-10-18
    Type: Refinement description