2Q71 | pdb_00002q71

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.199 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/10.1016/j.trsl.2006.08.006
  • Primary Citation Related Structures: 
    2Q6Z, 2Q71

  • 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 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

Macromolecule Content 

  • Total Structure Weight: 40.52 kDa 
  • Atom Count: 3,428 
  • Modeled Residue Count: 356 
  • Deposited Residue Count: 356 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uroporphyrinogen decarboxylase356Homo sapiensMutation(s): 1 
Gene Names: UROD
EC: 4.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P06132 (Homo sapiens)
Explore P06132 
Go to UniProtKB:  P06132
PHAROS:  P06132
GTEx:  ENSG00000126088 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06132
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CP3

Query on CP3



Download:Ideal Coordinates CCD File
B [auth A]COPROPORPHYRINOGEN III
C36 H44 N4 O8
NIUVHXTXUXOFEB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.199 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.037α = 90
b = 103.037β = 90
c = 71.865γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-03-12
    Changes: Non-polymer description
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.6: 2023-08-30
    Changes: Data collection, Refinement description