Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.86 kDa 
• Atom Count: 3273 
• Residue Count: 356 
• Unique protein chains: 1

2Q6Z

Uroporphyrinogen Decarboxylase G168R single mutant apo-enzyme

• DOI: 10.2210/pdb2Q6Z/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-06-05 Released: 2007-06-26 
• Deposition Author(s): Phillips, J.D., Whitby, F.G., Stadtmueller, B.M., Edwards, C.Q., Hill, C.P., Kushner, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.222 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Literature

Two novel uroporphyrinogen 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

• PubMed: 17240319 
• DOI: 10.1016/j.trsl.2006.08.006
• Primary Citation of Related Structures:  
  2Q71, 2Q6Z


• 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.

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Organizational Affiliation: 

Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uroporphyrinogen decarboxylase	A	356	Homo sapiens	Mutation(s): 1  Gene Names: UROD EC: 4.1.1.37
Find proteins for P06132 (Homo sapiens) Explore P06132  Go to UniProtKB:  P06132
NIH Common Fund Data Resources
PHAROS:  P06132 GTEx:  ENSG00000126088

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.222 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.236	α = 90
b = 103.236	β = 90
c = 72.398	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-06-05 
• Released Date: 2007-06-26 
Deposition Author(s): Phillips, J.D., Whitby, F.G., Stadtmueller, B.M., Edwards, C.Q., Hill, C.P., Kushner, J.P.

Revision History 

• Version 1.0: 2007-06-26
  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: 2017-10-18
  Changes: Refinement description