2LDB

STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE

Summary for 2LDB

• Entry DOI: 10.2210/pdb2ldb/pdb
• Descriptor: L-LACTATE DEHYDROGENASE, SULFATE ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (5 entities in total)
• Functional Keywords: oxidoreductase(choh(d)-nad(a))
• Biological source: Geobacillus stearothermophilus
• Cellular location: Cytoplasm: P00344
• Total number of polymer chains: 4
• Total formula weight: 143713.33

Authors

Piontek, K.,Rossmann, M.G. (deposition date: 1989-03-27, release date: 1989-07-12, Last modification date: 2023-09-27)

Primary citation

Piontek, K.,Chakrabarti, P.,Schar, H.P.,Rossmann, M.G.,Zuber, H.
Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase.
Proteins, 7:74-92, 1990

PubMed Abstract: Structures have been determined of Bacillus stearothermophilus "apo" and holo lactate dehydrogenase. The holo-enzyme had been co-crystallized with the activator fructose 1,6-bisphosphate. The "apo" lactate dehydrogenase structure was solved by use of the known apo-M4 dogfish lactate dehydrogenase molecule as a starting model. Phases were refined and extended from 4 A to 3 A resolution by means of the noncrystallographic molecular 222 symmetry. The R-factor was reduced to 28.7%, using 2.8 A resolution data, in a restrained least-squares refinement in which the molecular symmetry was imposed as a constraint. A low occupancy of coenzyme was found in each of the four subunits of the "apo"-enzyme. Further refinement proceeded with the isomorphous holo-enzyme from Bacillus stearothermophilus. After removing the noncrystallographic constraints, the R-factor dropped from 30.3% to a final value of 26.0% with a 0.019 A and 1.7 degrees r.m.s. deviation from idealized bond lengths and angles, respectively. Two sulfate ions per subunit were included in the final model of the "apo"-form--one at the substrate binding site and one close to the molecular P-axis near the location of the fructose 1,6-bisphosphate activator. The final model of the holo-enzyme incorporated two sulfate ions per subunit, one at the substrate binding site and another close to the R-axis. One nicotinamide adenine dinucleotide coenzyme molecule per subunit and two fructose 1,6-bisphosphate molecules per tetramer were also included. The phosphate positions of fructose 1,6-bisphosphate are close to the sulfate ion near the P-axis in the "apo" model. This structure represents the first reported refined model of an allosteric activated lactate dehydrogenase. The structure of the activated holo-enzyme showed far greater similarity to the ternary complex of dogfish M4 lactate dehydrogenase with nicotinamide adenine dinucleotide and oxamate than to apo-M4 dogfish lactate dehydrogenase. The conformations of nicotinamide adenine dinucleotide and fructose 1,6-bisphosphate were also analyzed.

PubMed: 2330370
DOI: 10.1002/prot.340070108

Experimental method

X-RAY DIFFRACTION (3 Å)