3Q3C

Crystal structure of a serine dehydrogenase from Pseudomonas aeruginosa pao1 in complex with NAD

Summary for 3Q3C

• Entry DOI: 10.2210/pdb3q3c/pdb
• Related: 3OBB
• Descriptor: Probable 3-hydroxyisobutyrate dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (3 entities in total)
• Functional Keywords: structural genomics, psi-2, protein structure initiative, midwest center for structural genomics, mcsg, alpha-beta fold, oxidoreductase
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 1
• Total formula weight: 32157.27

Authors

Tan, K.,Singer, A.U.,Evdokimova, E.,Kudritska, M.,Savchenko, A.,Edwards, A.M.,Joachimiak, A.,Yakunin, A.F.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2010-12-21, release date: 2011-02-23, Last modification date: 2024-10-30)

Primary citation

Tchigvintsev, A.,Singer, A.,Brown, G.,Flick, R.,Evdokimova, E.,Tan, K.,Gonzalez, C.F.,Savchenko, A.,Yakunin, A.F.
Biochemical and Structural Studies of Uncharacterized Protein PA0743 from Pseudomonas aeruginosa Revealed NAD+-dependent L-Serine Dehydrogenase.
J.Biol.Chem., 287:1874-1883, 2012

PubMed Abstract: The β-hydroxyacid dehydrogenases form a large family of ubiquitous enzymes that catalyze oxidation of various β-hydroxy acid substrates to corresponding semialdehydes. Several known enzymes include β-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, 2-(hydroxymethyl)glutarate dehydrogenase, and phenylserine dehydrogenase, but the vast majority of β-hydroxyacid dehydrogenases remain uncharacterized. Here, we demonstrate that the predicted β-hydroxyisobutyrate dehydrogenase PA0743 from Pseudomonas aeruginosa catalyzes an NAD(+)-dependent oxidation of l-serine and methyl-l-serine but exhibits low activity against β-hydroxyisobutyrate. Two crystal structures of PA0743 were solved at 2.2-2.3-Å resolution and revealed an N-terminal Rossmann fold domain connected by a long α-helix to the C-terminal all-α domain. The PA0743 apostructure showed the presence of additional density modeled as HEPES bound in the interdomain cleft close to the predicted catalytic Lys-171, revealing the molecular details of the PA0743 substrate-binding site. The structure of the PA0743-NAD(+) complex demonstrated that the opposite side of the enzyme active site accommodates the cofactor, which is also bound near Lys-171. Site-directed mutagenesis of PA0743 emphasized the critical role of four amino acid residues in catalysis including the primary catalytic residue Lys-171. Our results provide further insight into the molecular mechanisms of substrate selectivity and activity of β-hydroxyacid dehydrogenases.

PubMed: 22128181
DOI: 10.1074/jbc.M111.294561

Experimental method

X-RAY DIFFRACTION (2.299 Å)