Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 189.56 kDa 
• Atom Count: 14913 
• Residue Count: 1692 
• Unique protein chains: 1

3B8I

Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.

• DOI: 10.2210/pdb3B8I/pdb

• Classification: LYASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-11-01 Released: 2008-01-01 
• Deposition Author(s): Narayanan, B.C., Herzberg, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.249 
• R-Value Work: 0.191 
• R-Value Observed: 0.197 

Literature

Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily.

Narayanan, B.C., Niu, W., Han, Y., Zou, J., Mariano, P.S., Dunaway-Mariano, D., Herzberg, O.

(2008) Biochemistry 47: 167-182

• PubMed: 18081320 
• DOI: 10.1021/bi701954p
• Primary Citation of Related Structures:  
  3B8I


• PubMed Abstract: 
  

Pseudomonas aeruginosa PA4872 was identified by sequence analysis as a structurally and functionally novel member of the PEP mutase/isocitrate lyase superfamily and therefore targeted for investigation. Substrate screens ruled out overlap with known catalytic functions of superfamily members. The crystal structure of PA4872 in complex with oxalate (a stable analogue of the shared family alpha-oxyanion carboxylate intermediate/transition state) and Mg2+ was determined at 1.9 A resolution. As with other PEP mutase/isocitrate lyase superfamily members, the protein assembles into a dimer of dimers with each subunit adopting an alpha/beta barrel fold and two subunits swapping their barrel's C-terminal alpha-helices. Mg2+ and oxalate bind in the same manner as observed with other superfamily members. The active site gating loop, known to play a catalytic role in the PEP mutase and lyase branches of the superfamily, adopts an open conformation. The Nepsilon of His235, an invariant residue in the PA4872 sequence family, is oriented toward a C(2) oxygen of oxalate analogous to the C(3) of a pyruvyl moiety. Deuterium exchange into alpha-oxocarboxylate-containing compounds was confirmed by 1H NMR spectroscopy. Having ruled out known activities, the involvement of a pyruvate enolate intermediate suggested a decarboxylase activity of an alpha-oxocarboxylate substrate. Enzymatic assays led to the discovery that PA4872 decarboxylates oxaloacetate (kcat = 7500 s(-1) and Km = 2.2 mM) and 3-methyloxaloacetate (kcat = 250 s(-1) and Km = 0.63 mM). Genome context of the fourteen sequence family members indicates that the enzyme is used by select group of Gram-negative bacteria to maintain cellular concentrations of bicarbonate and pyruvate; however the decarboxylation activity cannot be attributed to a pathway common to the various bacterial species.

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Organizational Affiliation: 

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA4872 oxaloacetate decarboxylase	A, B, C, D, E, F	287	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: Dnase1, PA4872 EC: 4.1.1.3 (PDB Primary Data), 4.1.1.112 (UniProt)
Find proteins for Q9HUU1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUU1  Go to UniProtKB:  Q9HUU1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B, D, E, F	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXL	A, B, C, D, E, F	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L
MG	A, B, C, D, E, F	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
OXL	Ki:  4000   nM  Binding MOAD
OXL	Ki:  43000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.249 
• R-Value Work: 0.191 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 260.065	α = 90
b = 83.835	β = 112.14
c = 104.874	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-01 
• Released Date: 2008-01-01 
Deposition Author(s): Narayanan, B.C., Herzberg, O.

Revision History 

• Version 1.0: 2008-01-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary