Malate dehydrogenase (oxaloacetate-decarboxylating)

 

Malic enzymes are found in most living organisms, including bacteria and humans. They catalyse the conversion of L-malate to pyruvate with the concomitant reduction of the cofactor NAD+ or NADP+. In mammals three isoforms have been identified, a cytosolic NADP+ dependent enzyme, a mitochondrial NADP+ dependent enzyme and a mitochondrial NAD+ dependent enzyme. Each has a specific role, for example the mitochondrial NAD+ dependent enzyme is important for the metabolism of glutamine for energy production in rapidly proliferating tissues and tumours.

 

Reference Protein and Structure

Sequence
P23368 UniProt (1.1.1.38) IPR001891 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1do8 - CRYSTAL STRUCTURE OF A CLOSED FORM OF HUMAN MITOCHONDRIAL NAD(P)+-DEPENDENT MALIC ENZYME (2.2 Å) PDBe PDBsum 1do8
Catalytic CATH Domains
3.40.50.10380 CATHdb 3.40.50.720 CATHdb (see all for 1do8)
Cofactors
Manganese(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:1.1.1.38)

NADP(+)
CHEBI:18009ChEBI
+
(S)-malate(2-)
CHEBI:15589ChEBI
→
NADPH
CHEBI:16474ChEBI
+
carbon dioxide
CHEBI:16526ChEBI
+
pyruvate
CHEBI:15361ChEBI
Alternative enzyme names: Malic enzyme, NAD-linked malic enzyme, NAD-malic enzyme, NAD-specific malic enzyme, Pyruvic-malic carboxylase,

Enzyme Mechanism

Introduction

The catalysis by malate enzymes generally proceeds in two steps - dehydrogenation of the malate to produce oxaloacetate and then decarboxylation to produce pyruvate. A bound metal divalent cation (Mg2+ or Mn2+) polarises the C2 hydroxyl of malate for dehydrogenation and stabilises the C2 enolic oxygen for decarboxylation. Lys183 is the most likely candidate for a general acid to protonate the enol-pyruvate product of decarboxylation. Tyr112 plays a vital role in the dehydrogenation reaction although the structural basis for such a role is yet to be determined. Many other residues are involved in substrate binding and stabilisation.

Catalytic Residues Roles

UniProt PDB* (1do8)
Arg165, Asn421 Arg165(145)A, Asn421(401)A Acts as an electrostatic stabiliser throughout the reaction. hydrogen bond donor, electrostatic stabiliser
Lys183, Tyr112, Asp278 Lys183(163)A, Tyr112(92)A, Asp278(258)A Acts as a general acid/base at various points during the reaction. Initial protonation state is regenerated via an inferred return step. hydrogen bond donor, proton acceptor, proton donor, proton relay, electrostatic stabiliser
Asp279, Asp256, Glu255 Asp279(259)A, Asp256(236)A, Glu255(235)A Binds the Mn(II) ion. metal ligand
*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

hydride transfer, bimolecular elimination, aromatic bimolecular nucleophilic addition, overall reactant used, overall product formed, intermediate formation, proton transfer, unimolecular elimination by the conjugate base, decarboxylation, intermediate collapse, assisted keto-enol tautomerisation, intermediate terminated, proton relay, native state of enzyme regenerated, inferred reaction step

References

  1. Yang Z et al. (2000), Nat Struct Biol, 7, 251-257. Structure of a closed form of human malic enzyme and implications for catalytic mechanism. DOI:10.1038/73378. PMID:10700286.
  2. Tao X et al. (2003), Structure, 11, 1141-1150. Crystal Structures of Substrate Complexes of Malic Enzyme and Insights into the Catalytic Mechanism. DOI:10.1016/s0969-2126(03)00168-0. PMID:12962632.

Step 1. Asp278 deprotonates Lys183, which deprotonates the hydroxyl group of malate, which eliminates a hydride ion that is added to NADP.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp278(258)A hydrogen bond acceptor
Lys183(163)A proton relay, hydrogen bond donor
Asn421(401)A hydrogen bond donor, electrostatic stabiliser
Arg165(145)A hydrogen bond donor, electrostatic stabiliser
Tyr112(92)A hydrogen bond donor, electrostatic stabiliser
Asp256(236)A metal ligand
Glu255(235)A metal ligand
Asp279(259)A metal ligand
Asp278(258)A proton acceptor
Lys183(163)A proton donor, proton acceptor

Chemical Components

hydride transfer, ingold: bimolecular elimination, ingold: aromatic bimolecular nucleophilic addition, overall reactant used, overall product formed, intermediate formation, proton transfer

Step 2. The reduced intermediate decarboxylates with concomitant double bond rearrangement.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn421(401)A electrostatic stabiliser, hydrogen bond donor
Asp278(258)A hydrogen bond acceptor
Arg165(145)A hydrogen bond donor, electrostatic stabiliser
Lys183(163)A hydrogen bond donor, electrostatic stabiliser
Tyr112(92)A hydrogen bond donor, electrostatic stabiliser
Asp256(236)A metal ligand
Glu255(235)A metal ligand
Asp279(259)A metal ligand

Chemical Components

ingold: unimolecular elimination by the conjugate base, overall product formed, decarboxylation, intermediate collapse, intermediate formation

Step 3. The oxyanion collapses, reducing the C=C with concomitant deprotonation of Tyr112.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp278(258)A hydrogen bond acceptor
Tyr112(92)A hydrogen bond donor
Lys183(163)A hydrogen bond donor, electrostatic stabiliser
Asn421(401)A hydrogen bond donor, electrostatic stabiliser
Arg165(145)A hydrogen bond donor, electrostatic stabiliser
Asp256(236)A metal ligand
Glu255(235)A metal ligand
Asp279(259)A metal ligand
Tyr112(92)A proton donor

Chemical Components

assisted keto-enol tautomerisation, overall product formed, intermediate terminated, proton transfer

Step 4. Tyr112 deprotonates Lys183 which deprotonates Asp278 in an inferred return step.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys183(163)A hydrogen bond donor
Asp278(258)A hydrogen bond acceptor
Tyr112(92)A hydrogen bond acceptor
Asp256(236)A metal ligand
Glu255(235)A metal ligand
Asp279(259)A metal ligand
Lys183(163)A proton relay
Asp278(258)A proton donor
Tyr112(92)A proton acceptor
Lys183(163)A proton donor, proton acceptor

Chemical Components

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

Step 1. Asp278 deprotonates Lys183, which deprotonates the hydroxyl group of malate, which eliminates a hydride ion that is added to NADP.

Step 2. The reduced intermediate decarboxylates with concomitant double bond rearrangement.

Step 3. The oxyanion collapses, reducing the C=C with concomitant deprotonation of Tyr112.

Step 4. Tyr112 deprotonates Lys183 which deprotonates Asp278 in an inferred return step.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, Sophie T. Williams, James W. Murray, Craig Porter, Katherine Ferris