Jasper Lactate Final

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PDB ID 1i10

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1i10, resolution 2.30Å ()
Ligands: , ,
Gene: LDHA (Homo sapiens)
Activity: L-lactate dehydrogenase, with EC number 1.1.1.27
Related: 1i0z, 9ldt, 5ldh, 1ldg
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



Contents

HUMAN MUSCLE L-LACTATE DEHYDROGENASE M CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE

Lactate Dehydrogenase

is an important enzyme in humans. It occurs in different regions of the body, each region having a unique conformation of different subunits. The Jmole image shown is that of LDH-5, the form found in skeleton muscle and the liver. LDH is a key enzyme in anaerobic respiration. Anaerobic Respiration is the conversion of pyruvate into lactate acid in the absence oxygen. This pathway is important to glycolysis in two main ways. The first is that if pyruvate were to build up glycoysis and thus the generation of ATP would slow. The second is anaerobic respiration allows for the regeneration of NAD+ from NADH. NAD+ is required when glyceraldehyde-3-phosphate dehydrogenase oxidizes glyceraldehyde-3-phosphate in glycolysis, which generates NADH. Lactate dehydrogenase is responsible for the anaerobic conversion of NADH to NAD+. Catalytic function of LDH (1)

Structure

LDH is a quaternary protein formed of the combination of two subunits, M and H (Muscle and Heart) into a structure of four of the subunits. The various combinations found in the human body are:

  • (4H) Heart
  • (3H1M) Reticuloendothelial
  • (2H2M) Lungs
  • (1H3M) Kidneys
  • (4M) Muscle and Liver

The of LDH as shown here is comprised of 40% alpha helices and 23% beta sheets[1]. The SCOP data classifies this form of lactate dehydrogenase as mixed beta-alpha-beta, with mainly parallel beta sheets.


Catalysis

Studies have shown that the reaction mechanism of LDH follows an ordered sequence. In order for lactate to be oxidized NADH must bind to the enzyme first followed by lactate. Several residues are involved in the binding of NADH, including and . Once the NADH is bound to the enzyme, it is then possible for lactate to bind. Lactate binds to the enzyme between the nicotinamide ring and . Transfer of a hydride ion then happens quickly in either direction giving a mixture of the two tertiary complexes, enzyme-NAD+-lactate and enzyme-NADH-pyruvate .Finally pyruvate dissociates from the enzyme followed by NAD+[2].

(1)

Kinetics

Kinetic studies of lactate dehydrogenase with oxalate and oxamate (structural analogues of lactate and pyruvate)have proven the mechanism stated above. The rate limiting step in this reaction is the rate of dissociation of NAD+ and NADH. The conversion of pyruvate to lactate with the subsequent regeneration of NAD+ is very favorable.

(1)

Regulation

As the mechanism is one of equilibrium, There appears to be no regulation specifically designed for lactate dehydrogenase, instead it is dependent on the activation of anaerobic reparation and the presence of pyruvate and NADH, or lactate and NAD+.


Reference

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