1J4A

INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS

Summary for 1J4A

• Entry DOI: 10.2210/pdb1j4a/pdb
• Descriptor: D-LACTATE DEHYDROGENASE, SULFATE ION (3 entities in total)
• Functional Keywords: nad-dependent dehydrogenase, reversible interconversion of pyruvate into d-lactate, oxidoreductase
• Biological source: Lactobacillus delbrueckii subsp. bulgaricus
• Total number of polymer chains: 4
• Total formula weight: 149505.33

Authors

Razeto, A.,Kochhar, S.,Hottinger, H.,Dauter, M.,Wilson, K.S.,Lamzin, V.S. (deposition date: 2001-08-18, release date: 2002-05-29, Last modification date: 2024-04-03)

Primary citation

Razeto, A.,Kochhar, S.,Hottinger, H.,Dauter, M.,Wilson, K.S.,Lamzin, V.S.
Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus.
J.Mol.Biol., 318:109-119, 2002

PubMed Abstract: 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.

PubMed: 12054772
DOI: 10.1016/S0022-2836(02)00086-4

Experimental method

X-RAY DIFFRACTION (1.9 Å)