3GW0 | pdb_00003gw0

UROD mutant G318R

• PDB DOI: https://doi.org/10.2210/pdb3GW0/pdb

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


• Deposited: 2009-03-31 Released: 2009-07-07 
• Deposition Author(s): Hill, C.P., Phillips, J.D., Whitby, F.G., Warby, C., Kushner, J.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.240 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Structural and kinetic characterization of mutant human uroporphyrinogen decarboxylases.

Warby, C.A., Phillips, J.D., Bergonia, H.A., Whitby, F.G., Hill, C.P., Kushner, J.P.

(2009) Cell Mol Biol (noisy-le-grand) 55: 40-45

• PubMed: 19656450 
• Primary Citation Related Structures: 
  3GW0, 3GW3


• PubMed Abstract: 
  

  Porphyria cutanea tarda (PCT) is caused by inhibition of uroporphyrinogen decarboxylase (URO-D) activity in hepatocytes. Subnormal URO-D activity results in accumulation and urinary excretion of uroporphyrin and heptacarboxyl porphyrin. Heterozygosity for mutations in the URO-D gene is found in the familial form of PCT (F-PCT). Over 70 mutations of URO-D have been described but very few have been characterized structurally. Here we characterize 3 mutations in the URO-D gene found in patients with F-PCT, G318R, K297N, and D306Y. Expression of the D306Y mutation results in an insoluble recombinant protein. G318R and K297N have little effect on the structure or activity of recombinant URO-D, but the proteins display reduced stability in vitro.

---

Organizational Affiliation: 
• Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.93 kDa 
• Atom Count: 2,985 
• Modeled Residue Count: 356 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uroporphyrinogen decarboxylase	A	367	Homo sapiens	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.240 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.266	α = 90
b = 103.266	β = 90
c = 73.389	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

• Released Date: 2009-07-07 
Deposition Author(s): Hill, C.P., Phillips, J.D., Whitby, F.G., Warby, C., Kushner, J.P.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-03-12
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2021-10-13
  Changes: Database references
• Version 1.5: 2024-02-21
  Changes: Data collection