L-lactate dehydrogenase

 

Lactate dehydrogenase catalyses the interconversion of L-lactate and pyruvate in the glycolytic pathway, coupled with the reduction/oxidation of NAD+ and NADH. The enzyme crystallised from dogfish is a homotetramer. There has been some debate about whether the enzyme mechanism is concerted or stepwise.

 

Reference Protein and Structure

Sequence
P00341 UniProt (1.1.1.27) IPR011304 (Sequence Homologues) (PDB Homologues)
Biological species
Squalus acanthias (spiny dogfish) Uniprot
PDB
1ldm - Refined crystal structure of dogfish M4 apo-lactate dehydrogenase (2.1 Å) PDBe PDBsum 1ldm
Catalytic CATH Domains
3.90.110.10 CATHdb 3.40.50.720 CATHdb (see all for 1ldm)
Click To Show Structure

Enzyme Reaction (EC:1.1.1.27)

(S)-lactate
CHEBI:16651ChEBI
+
NAD(1-)
CHEBI:57540ChEBI
→
pyruvate
CHEBI:15361ChEBI
+
hydron
CHEBI:15378ChEBI
+
NADH(2-)
CHEBI:57945ChEBI
Alternative enzyme names: L(+)-nLDH, L-(+)-lactate dehydrogenase, L-lactic acid dehydrogenase, L-lactic dehydrogenase, NAD-lactate dehydrogenase, Lactate dehydrogenase, Lactate dehydrogenase NAD-dependent, Lactic acid dehydrogenase, Lactic dehydrogenase,

Enzyme Mechanism

Introduction

In the forward direction a proton is abstracted from lactate and a hydride donated to NAD+. In the reverse direction a proton is donated to pyruvate and a hydride ion donated from NADH. The proton donor/abstractor depending on direction is His193, which is regulated via hydrogen-bond to Asp166. The hydride is donated/abstracted by NADH/NAD+. It is likely that the reaction proceeds in a stepwise manner with Arg169 stabilising the charge via a strong salt bridge to the substrate, and possibly via electrostatic interactions from Arg106.

Catalytic Residues Roles

UniProt PDB* (1ldm)
His194 His193A Acts as a general acid/base. proton acceptor, proton donor
Arg107, Arg170 Arg106A, Arg169A Stabilise the reactive intermediates and transition states formed during the course of the reaction. electrostatic stabiliser
Asp167 Asp166A Forms a dyad with His193, enhancing its reactivity. enhance reactivity
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, hydride transfer, overall reactant used, overall product formed, cofactor used, native state of enzyme regenerated, inferred reaction step

References

  1. Abad-Zapatero C et al. (1987), J Mol Biol, 198, 445-467. Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. DOI:10.1016/0022-2836(87)90293-2. PMID:3430615.
  2. Cameron A et al. (2004), J Biol Chem, 279, 31429-31439. Identification and activity of a series of azole-based compounds with lactate dehydrogenase-directed anti-malarial activity. DOI:10.1074/jbc.M402433200. PMID:15117937.

Step 1. His193 abstracts a proton from the hydroxyl group of the substrate. NAD accepts a hydride in a nucleophilic addition reaction.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp166A enhance reactivity
Arg106A electrostatic stabiliser
Arg169A electrostatic stabiliser
His193A proton acceptor

Chemical Components

proton transfer, hydride transfer, overall reactant used, overall product formed, cofactor used

Step 2. In an inferred step his193 is deprotonated to regenerate the native state of the enzyme.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His193A proton donor

Chemical Components

proton transfer, native state of enzyme regenerated, inferred reaction step
Download: Image, Marvin File

Step 1. His193 abstracts a proton from the hydroxyl group of the substrate. NAD accepts a hydride in a nucleophilic addition reaction.

Step 2. In an inferred step his193 is deprotonated to regenerate the native state of the enzyme.

Products.

Contributors

Anna Waters, Craig Porter, Gemma L. Holliday, Amelia Brasnett