1LOL | pdb_00001lol

Crystal structure of orotidine monophosphate decarboxylase complex with XMP

• PDB DOI: https://doi.org/10.2210/pdb1LOL/pdb

• Classification: LYASE
• Organism(s): Methanothermobacter thermautotrophicus str. Delta H
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-06 Released: 2002-08-07 
• Deposition Author(s): Wu, N., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5'-monophosphate decarboxylase.

Wu, N., Pai, E.F.

(2002) J Biological Chem 277: 28080-28087

• PubMed: 12011084 
• DOI: https://doi.org/10.1074/jbc.M202362200
• Primary Citation Related Structures: 
  1LOL, 1LOQ, 1LOR, 1LOS, 1LP6


• PubMed Abstract: 
  

  The crystal structures of the enzyme orotidine-5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with its product UMP and the inhibitors 6-hydroxyuridine 5'-phosphate (BMP), XMP, and CMP are reported. A mutant version of the protein, in which four residues of the flexible phosphate-binding loop (180)Gly-Gly(190) were removed and Arg(203) was replaced by alanine, was also analyzed. The XMP and CMP complexes reveal a ligand-binding mode that is distinct from the one identified previously with the aromatic rings located outside the binding pocket. A potential pathway for ligand binding is discussed.

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Organizational Affiliation: 
• Department of Biochemistry, University of Toronto, Ontario M5S 1A8, 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: 50.9 kDa 
• Atom Count: 3,431 
• Modeled Residue Count: 418 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
orotidine 5'-monophosphate decarboxylase	A, B	229	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0  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
XMP	D [auth A], F [auth B]	XANTHOSINE-5'-MONOPHOSPHATE C10 H14 N4 O9 P DCTLYFZHFGENCW-UUOKFMHZSA-O
BU2	C [auth A], E [auth B]	1,3-BUTANEDIOL C4 H10 O2 PUPZLCDOIYMWBV-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.57	α = 90
b = 55.482	β = 94.28
c = 66.129	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-07 
Deposition Author(s): Wu, N., Pai, E.F.

Revision History  

• Version 1.0: 2002-08-07
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations