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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.39 kDa 
• Atom Count: 4737 
• Modelled Residue Count: 514 
• Deposited Residue Count: 520 
• Unique protein chains: 1

3EWW

D312N mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-cyano-UMP, covalent adduct

• DOI: 10.2210/pdb3EWW/pdb

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


• Deposited: 2008-10-16 Released: 2009-04-07 
• Deposition Author(s): Heinrich, D., Wittmann, J., Diederichsen, U., Rudolph, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.187 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Literature

Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase

Heinrich, D., Diederichsen, U., Rudolph, M.G.

(2009) Chemistry 15: 6619-6625

• PubMed: 19472232 
• DOI: 10.1002/chem.200900397
• Primary Citation of Related Structures:  
  3L0K, 3L0N, 3EWU, 3EX6, 3EWW, 3EWX, 3EWY, 3EWZ, 3EX1, 3EX2


• PubMed Abstract: 
  

Orotidine-5'-monophosphate decarboxylase (OMPD) catalyzes the decarboxylation of orotidine-5'-monophosphate (OMP) to uridine-5'-monophosphate (UMP) in an extremely proficient manner. The reaction does not require any cofactors and proceeds by an unknown mechanism. In addition to decarboxylation, OMPD is able to catalyze other reactions. We show that several C6-substituted UMP derivatives undergo hydrolysis or substitution reactions that depend on a lysine residue (Lys314) in the OMPD active site. 6-Cyano-UMP is converted to UMP, and UMP derivatives with good leaving groups inhibit OMPD by a suicide mechanism in which Lys314 covalently binds to the substrate. These non-classical reactivities of human OMPD were characterized by cocrystallization and freeze-trapping experiments with wild-type OMPD and two active-site mutants by using substrate and inhibitor nucleotides. The structures show that the C6-substituents are not coplanar with the pyrimidine ring. The extent of this substrate distortion is a function of the substituent geometry. Structure-based mechanisms for the reaction of 6-substituted UMP derivatives are extracted in accordance with results from mutagenesis, mass spectrometry, and OMPD enzyme activity. The Lys314-based mechanisms explain the chemodiversity of OMPD, and offer a strategy to design mechanism-based inhibitors that could be used for antineoplastic purposes for example.

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Organizational Affiliation: 

Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine-5'-phosphate decarboxylase	A, B	260	Homo sapiens	Mutation(s): 1  Gene Names: UMPS, OK/SW-cl.21 EC: 4.1.1.23 (PDB Primary Data), 2.4.2.10 (UniProt)
Find proteins for P11172 (Homo sapiens) Explore P11172  Go to UniProtKB:  P11172
NIH Common Fund Data Resources
PHAROS:  P11172 GTEx:  ENSG00000114491

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U1P	D [auth A], E [auth B]	6-[(E)-iminomethyl]uridine 5'-phosphate C10 H14 N3 O9 P GSNYQYNODBCZBM-XDMCGQROSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.187 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.527	α = 90
b = 61.479	β = 113.13
c = 70.491	γ = 90

Software Package:

Software Name	Purpose
COMO	phasing
REFMAC	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-10-16 
• Released Date: 2009-04-07 
Deposition Author(s): Heinrich, D., Wittmann, J., Diederichsen, U., Rudolph, M.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description