Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.91 kDa 
• Atom Count: 3088 
• Residue Count: 357 
• Unique protein chains: 1

1URO

UROPORPHYRINOGEN DECARBOXYLASE

• DOI: 10.2210/pdb1URO/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1998-08-21 Released: 1998-08-26 
• Deposition Author(s): Whitby, F.G., Phillips, J.D., Kushner, J.P., Hill, C.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

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

• PubMed: 9564029 
• DOI: 10.1093/emboj/17.9.2463
• Primary Citation of Related Structures:  
  1URO


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (UROPORPHYRINOGEN DECARBOXYLASE)	A	367	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	A	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103	α = 90
b = 103	β = 90
c = 73.7	γ = 120

Software Package:

Software Name	Purpose
XTALVIEW	refinement
PHASES	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-08-21 
• Released Date: 1998-08-26 
Deposition Author(s): Whitby, F.G., Phillips, J.D., Kushner, J.P., Hill, C.P.

Revision History 

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