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: 43.35 kDa 
• Atom Count: 2983 
• Residue Count: 357 
• Unique protein chains: 1

1JPH

Ile260Thr mutant of Human UroD, human uroporphyrinogen III decarboxylase

• DOI: 10.2210/pdb1JPH/pdb

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


• Deposited: 2001-08-02 Released: 2001-12-19 
• Deposition Author(s): Phillips, J.D., Parker, T.L., Schubert, H.L., Whitby, F.G., Hill, C.P., Kushner, J.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 

Literature

Functional consequences of naturally occurring mutations in human uroporphyrinogen decarboxylase.

Phillips, J.D., Parker, T.L., Schubert, H.L., Whitby, F.G., Hill, C.P., Kushner, J.P.

(2001) Blood 98: 3179-3185

• PubMed: 11719352 
• DOI: 10.1182/blood.v98.12.3179
• Primary Citation of Related Structures:  
  1JPK, 1JPI, 1JPH


• PubMed Abstract: 
  

Functional consequences of 12 mutations-10 missense, 1 splicing defect, and 1 frameshift mutation-were characterized in the uroporphyrinogen decarboxylase (URO-D) gene found in Utah pedigrees with familial porphyria cutanea tarda (F-PCT). All but one mutation altered a restriction site in the URO-D gene, permitting identification of affected relatives using a combination of polymerase chain reaction and restriction enzyme digestion. In a bacterial expression system, 3 of the missense mutants were found in inclusion bodies, but 7 were expressed as soluble proteins. Enzymatic activity of soluble, recombinant mutant URO-D genes ranged from 29% to 94% of normal. URO-D mRNA levels in Epstein-Barr-virus transformed cells derived from patients were normal (with the exception of the frameshift mutation) even though protein levels were lower than normal, suggesting that missense mutations generally cause unstable URO-Ds in vivo. The crystal structures of 3 mutant URO-Ds were solved, and the structural consequences of the mutations were defined. All missense mutations reported here and by others were mapped to the crystal structure of URO-D, and structural effects were predicted. These studies define structural and functional consequences of URO-D mutations occurring in patients with F-PCT.

---

Related Citations: 

• Crystal Structure of Human Uroporphyrinogen Decarboxylase
  Whitby, F.G., Phillips, J.D., Kushner, J.P., Hill, C.P.
  (1998) EMBO J 17: 2463

---

Organizational Affiliation: 

Department of Medicine, University of Utah School of Medicine, Salt Lake City 84132, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UROPORPHYRINOGEN DECARBOXYLASE	A	388	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: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.14	α = 90
b = 103.14	β = 90
c = 73.32	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-08-02 
• Released Date: 2001-12-19 
Deposition Author(s): Phillips, J.D., Parker, T.L., Schubert, H.L., Whitby, F.G., Hill, C.P., Kushner, J.P.

Revision History 

• Version 1.0: 2001-12-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance