2ldb
From Proteopedia
|
STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE
Overview
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.
About this Structure
2LDB is a Single protein structure of sequence from Geobacillus stearothermophilus with FBP, SO4 and NAD as ligands. Active as L-lactate dehydrogenase, with EC number 1.1.1.27 Full crystallographic information is available from OCA.
Reference
Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase., Piontek K, Chakrabarti P, Schar HP, Rossmann MG, Zuber H, Proteins. 1990;7(1):74-92. PMID:2330370
Page seeded by OCA on Wed Nov 21 12:41:36 2007
