Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.43 kDa 
• Atom Count: 3428 
• Residue Count: 356 
• Unique protein chains: 1

1R3S

Uroporphyrinogen Decarboxylase single mutant D86G in complex with coproporphyrinogen-I

• DOI: 10.2210/pdb1R3S/pdb

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


• Deposited: 2003-10-03 Released: 2003-12-09 
• Deposition Author(s): Phillips, J.D., Whitby, F.G., Kushner, J.P., Hill, C.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.190 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 

Literature

Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase

Phillips, J.D., Whitby, F.G., Kushner, J.P., Hill, C.P.

(2003) EMBO J 22: 6225-6233

• PubMed: 14633982 
• DOI: 10.1093/emboj/cdg606
• Primary Citation of Related Structures:  
  1R3Q, 1R3Y, 1R3W, 1R3V, 1R3T, 1R3S, 1R3R


• PubMed Abstract: 
  

Uroporphyrinogen decarboxylase (URO-D), an essential enzyme that functions in the heme biosynthetic pathway, catalyzes decarboxylation of all four acetate groups of uroporphyrinogen to form coproporphyrinogen. Here we report crystal structures of URO-D in complex with the I and III isomer coproporphyrinogen products. Crystallization required use of a novel enzymatic approach to generate the highly oxygen-sensitive porphyrinogen substrate in situ. The tetrapyrrole product adopts a domed conformation that lies against a collar of conserved hydrophobic residues and allows formation of hydrogen bonding interactions between a carboxylate oxygen atom of the invariant Asp86 residue and the pyrrole NH groups. Structural and biochemical analyses of URO-D proteins mutated at Asp86 support the conclusion that this residue makes important contributions to binding and likely promotes catalysis by stabilizing a positive charge on a reaction intermediate. The central coordination geometry of Asp86 allows the initial substrates and the various partially decarboxylated intermediates to be bound with equivalent activating interactions, and thereby explains how all four of the substrate acetate groups can be decarboxylated at the same catalytic center.

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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	367	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1CP	A	COPROPORPHYRINOGEN I C36 H44 N4 O8 WIUGGJKHYQIGNH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.190 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.947	α = 90
b = 102.947	β = 90
c = 72.585	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-03 
• Released Date: 2003-12-09 
Deposition Author(s): Phillips, J.D., Whitby, F.G., Kushner, J.P., Hill, C.P.

Revision History 

• Version 1.0: 2003-12-09
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-03-12
  Changes: Non-polymer description