1X1Z

Orotidine 5'-monophosphate decarboxylase (odcase) complexed with BMP (produced from 6-cyanoump)

• PDB DOI: https://doi.org/10.2210/pdb1X1Z/pdb

• Classification: LYASE
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-04-15 Released: 2005-12-06 
• Deposition Author(s): Fujihashi, M., Bello, A.M., Poduch, E., Wei, L., Annedi, S.C., Pai, E.F., Kotra, L.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.180 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 

Literature

An unprecedented twist to ODCase catalytic activity

Fujihashi, M., Bello, A.M., Poduch, E., Wei, L., Annedi, S.C., Pai, E.F., Kotra, L.P.

(2005) J Am Chem Soc 127: 15048-15050

• PubMed: 16248642 
• DOI: https://doi.org/10.1021/ja054865u
• Primary Citation of Related Structures:  
  1X1Z


• PubMed Abstract: 
  

  Orotidine-5'-monophosphate decarboxylase (ODCase) has evolved to catalyze a decarboxylation reaction, most probably via a carbanion species at the C6 position of orotidine-5'-monophosphate. We reveal an unusual biochemical pathway of conversion of 6-cyano-uridine-5'-monophosphate by ODCase to barbiturate-5'-monophosphate via perhaps an electrophilic center at the C6 position, leading to inhibition. This potential of ODCase is very useful in the design of novel inhibitors.

---

Organizational Affiliation: 

Molecular Design and Information Technology Center, Leslie Dan Faculty of Pharmacy, Toronto, ON M5S 2S2 Canada.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 55.81 kDa 
• Atom Count: 3,738 
• Modelled Residue Count: 430 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	252	Methanothermobacter thermautotrophicus	Mutation(s): 2  EC: 4.1.1.23
UniProt
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26232  Go to UniProtKB:  O26232

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMP	C [auth A], D [auth A]	6-HYDROXYURIDINE-5'-PHOSPHATE C9 H13 N2 O10 P UDOBICLZEKUKCV-YXZULKJRSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BMP	PDBBind:  1X1Z	Ki: 8.80e-3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.180 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.105	α = 90
b = 73.568	β = 119.28
c = 59.399	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-06 
Deposition Author(s): Fujihashi, M., Bello, A.M., Poduch, E., Wei, L., Annedi, S.C., Pai, E.F., Kotra, L.P.

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection