Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 123862.43 
• Atom Count: 8452 
• Residue Count: 1128 
• Unique protein chains: 1

2Q28

Crystal structure of oxalyl-coA decarboxylase from Escherichia coli in complex with adenosine-5`-diphosphate

• DOI: 10.2210/pdb2Q28/pdb

• Classification: LYASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 2007-05-26 Released: 2008-06-03 
• Deposition Author(s): Werther, T., Zimmer, A., Wille, G., Hubner, G., Weiss, M.S., Konig, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.196 
• R-Value Work: 0.177 

Literature

New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli.

Werther, T., Zimmer, A., Wille, G., Golbik, R., Weiss, M.S., Konig, S.

(2010) Febs J. 277: 2628-2640

• PubMed: 20553497 
• DOI: 10.1111/j.1742-464X.2010.07673.x
• Primary Citation of Related Structures:  
  2Q29, 2Q27


• PubMed Abstract: 
  

The gene yfdU from Escherichia coli encodes a putative oxalyl coenzyme A decarboxylase, a thiamine diphosphate-dependent enzyme that is potentially involved in the degradation of oxalate. The enzyme has been purified to homogeneity. The kinetic constants for conversion of the substrate oxalyl coenzyme A by the enzyme in the absence and presence of the inhibitor coenzyme A, as well as in the absence and presence of the activator adenosine 5'-diphosphate, were determined using a novel continuous optical assay. The effects of these ligands on the solution and crystal structure of the enzyme were studied using small-angle X-ray scattering and X-ray crystal diffraction. Analyses of the obtained crystal structures of the enzyme in complex with the cofactor thiamine diphosphate, the activator adenosine 5'-diphosphate and the inhibitor acetyl coenzyme A, as well as the corresponding solution scattering patterns, allow comparison of the oligomer structures of the enzyme complexes under various experimental conditions, and provide insights into the architecture of substrate and effector binding sites.

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Organizational Affiliation: 

Department of Enzymology, Institute of Biochemistry & Biotechnology, Faculty for Biological Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
oxalyl-CoA decarboxylase	A, B	564	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: oxc (yfdU) EC: 4.1.1.8
Find proteins for P0AFI0 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AFI0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TPP	A, B	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ADP	A, B	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
EDO	A, B	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
MES	A, B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.196 
• R-Value Work: 0.177 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 132.270	α = 90.00
b = 143.620	β = 90.00
c = 147.580	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-26 
• Released Date: 2008-06-03 
• Deposition Author(s): Werther, T., Zimmer, A., Wille, G., Hubner, G., Weiss, M.S., Konig, S.

Revision History 

• Version 1.0: 2008-06-03
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-10-18
  Type: Refinement description