Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106.87 kDa 
• Atom Count: 7474 
• Modelled Residue Count: 925 
• Deposited Residue Count: 980 
• Unique protein chains: 1

1EIX

STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP

• PDB DOI: 10.2210/pdb1EIX/pdb

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


• Deposited: 2000-02-29 Released: 2000-03-15 
• Deposition Author(s): Harris, P., Poulsen, J.C.N., Jensen, K.F., Larsen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.264 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase.

Harris, P., Poulsen, J.C.N., Jensen, K.F., Larsen, S.

(2000) Biochemistry 39: 4217-4224

• PubMed: 10757968 
• DOI: 10.1021/bi992952r
• Primary Citation of Related Structures:  
  1EIX


• PubMed Abstract: 
  

Orotidine 5'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine 5'-monophosphate, the last step in the de novo synthesis of uridine 5'-monophosphate. ODCase is a very proficient enzyme [Radzicka, A., and Wolfenden, R. (1995) Science 267, 90-93], enhancing the reaction rate by a factor of 10(17). This proficiency has been enigmatic, since it is achieved without metal ions or cofactors. Here we present a 2.5 A resolution structure of ODCase complexed with the inhibitor 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid. It shows a closely packed dimer composed of two alpha/beta-barrels with two shared active sites. The orientation of the orotate moiety of the substrate is unambiguously deduced from the structure, and previously proposed catalytic mechanisms involving protonation of O2 or O4 can be ruled out. The proximity of the OMP carboxylate group with Asp71 appears to be instrumental for the decarboxylation of OMP, either through charge repulsion or through the formation of a very short O.H.O hydrogen bond between the two carboxylate groups.

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Organizational Affiliation: 

Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE	A, B, C, D	245	Escherichia coli	Mutation(s): 0  EC: 4.1.1.23
UniProt
Find proteins for P08244 (Escherichia coli (strain K12)) Explore P08244  Go to UniProtKB:  P08244

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMQ	E [auth A], F [auth B], G [auth C], H [auth D]	1-(5'-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID C9 H13 N2 O10 P AODYJUNLDJOADV-YXZULKJRSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BMQ	PDBBind:  1EIX	Ki: 8.80e-3 (nM) from 1 assay(s)
	Binding MOAD:  1EIX	Ki: 8.80e-3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.264 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.28	α = 90
b = 95.92	β = 90
c = 145.02	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
SOLVE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-02-29 
• Released Date: 2000-03-15 
Deposition Author(s): Harris, P., Poulsen, J.C.N., Jensen, K.F., Larsen, S.

Revision History  

• Version 1.0: 2000-03-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection