1j4a
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INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS
OverviewOverview
NAD-dependent Lactobacillus bulgaricus D-Lactate dehydrogenase (D-LDHb), catalyses the reversible conversion of pyruvate into D-lactate. Crystals, of D-LDHb complexed with NADH were grown and X-ray data collected to 2.2, A. The structure of D-LDHb was solved by molecular replacement using the, dimeric Lactobacillus helveticus D-LDH as a model and was refined to an, R-factor of 20.7%. The two subunits of the enzyme display strong asymmetry, due to different crystal environments. The opening angles of the two, catalytic domains with respect to the core coenzyme binding domains differ, by 16 degrees. Subunit A is in an "open" conformation typical for a, dehydrogenase apo enzyme and subunit B is "closed". The NADH-binding site, in subunit A is only 30% occupied, while in subunit B it is fully occupied, and there is a sulphate ion in the substrate-binding pocket. A pyruvate, molecule has been modelled in the active site and its orientation is in, agreement with existing kinetic and structural data. On domain closure, a, cluster of hydrophobic residues packs tightly around the methyl group of, the modelled pyruvate molecule. At least three residues from this cluster, govern the substrate specificity. Substrate binding itself contributes to, the stabilisation of domain closure and activation of the enzyme. In, pyruvate reduction, D-LDH can adapt another protonated residue, a lysine, residue, to accomplish the role of the acid catalyst His296. Required, lowering of the lysine pK(a) value is explained on the basis of the H296K, mutant structure.
About this StructureAbout this Structure
1J4A is a Single protein structure of sequence from Lactobacillus delbrueckii subsp. bulgaricus with SO4 as ligand. Active as D-lactate dehydrogenase, with EC number 1.1.1.28 Full crystallographic information is available from OCA.
ReferenceReference
Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus., Razeto A, Kochhar S, Hottinger H, Dauter M, Wilson KS, Lamzin VS, J Mol Biol. 2002 Apr 19;318(1):109-19. PMID:12054772
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