1URO

UROPORPHYRINOGEN DECARBOXYLASE

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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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) ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (UROPORPHYRINOGEN DECARBOXYLASE)A367Homo sapiensMutation(s): 0 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME
Download Ideal Coordinates CCD File 
 B [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N		 Ligand Interaction
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 = 103α = 90
b = 103β = 90
c = 73.7γ = 120
Software Package:
Software NamePurpose
XTALVIEWrefinement
PHASESphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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