3B8I

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

Summary for 3B8I

• Entry DOI: 10.2210/pdb3b8i/pdb
• Descriptor: PA4872 oxaloacetate decarboxylase, MAGNESIUM ION, OXALATE ION, ... (5 entities in total)
• Functional Keywords: alpha/beta barrel, helix swapping, lyase
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 6
• Total formula weight: 189563.78

Authors

Narayanan, B.C.,Herzberg, O. (deposition date: 2007-11-01, release date: 2008-01-01, Last modification date: 2024-02-21)

Primary citation

Narayanan, B.C.,Niu, W.,Han, Y.,Zou, J.,Mariano, P.S.,Dunaway-Mariano, D.,Herzberg, O.
Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily.
Biochemistry, 47:167-182, 2008

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.

PubMed: 18081320
DOI: 10.1021/bi701954p

Experimental method

X-RAY DIFFRACTION (1.9 Å)