Methylenetetrahydrofolate dehydrogenase (NADP+)

 

Enzymes involved in tetrahydrofolate metabolism are of particular pharmaceutical interest, as their function is crucial for amino acid and DNA biosynthesis.

In eukaryotes, the enzyme that performs this reaction occurs as a trifunctional enzyme that also has methylenetetrahydrofolate dehydrogenase (NADP+) (EC 1.5.1.5) and formate-tetrahydrofolate ligase (EC 6.3.4.3) activity. In some prokaryotes, it occurs as a bifunctional enzyme that also has dehydrogenase (EC 1.5.1.5) activity or formiminotetrahydrofolate cyclodeaminase (EC 4.3.1.4) activity. This particular entry represents the dehydrogenase activity.

Although the human protein represented here is actually trifunctional, the representative PDB structure only contains the dehydrogenase (D) and cyclohydrolase (C) domains, which have an overlapping active site (as determined by chemical modification and kinetic studies).

 

Reference Protein and Structure

Sequence
P11586 UniProt (1.5.1.5, 3.5.4.9, 6.3.4.3) IPR000672 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1a4i - HUMAN TETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE (1.5 Å) PDBe PDBsum 1a4i
Catalytic CATH Domains
3.40.50.10860 CATHdb (see all for 1a4i)
Click To Show Structure

Enzyme Reaction (EC:1.5.1.5)

NADP(+)
CHEBI:18009ChEBI
+
5,10-methylenetetrahydrofolate(2-)
CHEBI:12071ChEBI
→
NADH
CHEBI:16908ChEBI
+
(6R)-5,10-methenyltetrahydrofolate
CHEBI:57455ChEBI
Alternative enzyme names: 5,10-methylenetetrahydrofolate dehydrogenase, 5,10-methylenetetrahydrofolate:NADP oxidoreductase, N(5),N(10)-methylenetetrahydrofolate dehydrogenase, Methylenetetrahydrofolate dehydrogenase, Methylenetetrahydrofolate dehydrogenase (NADP),

Enzyme Mechanism

Introduction

5,10-methylene-tetrahydrofolate is converted to 5,10-methenyltetrahydrofolate. The mechanism involves hydride transfer from the substrate to NADP+.

Catalytic Residues Roles

UniProt PDB* (1a4i)
Gln100 Gln100A Lowers pKa of Lys56. activator
Lys56 Lys56A Lys56 amino group increases the electron density in the tetrahydropteridine moiety, activating it and thereby assisting the abstraction of a hydride from the methylene group by the nicotinamide moiety of NADP. activator
Asp125 Asp125A Helps stabilise the reactive intermediates and transition states. electrostatic stabiliser
*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

References

  1. Schmidt A et al. (2000), Biochemistry, 39, 6325-6335. Structures of Three Inhibitor Complexes Provide Insight into the Reaction Mechanism of the Human Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase. DOI:10.1021/bi992734y. PMID:10828945.
  2. Sah S et al. (2015), Biochemistry, 54, 3504-3513. Impact of Mutating the Key Residues of a Bifunctional 5,10-Methylenetetrahydrofolate Dehydrogenase-Cyclohydrolase fromEscherichia colion Its Activities. DOI:10.1021/acs.biochem.5b00400. PMID:25988590.
  3. Wagner W et al. (2005), Biochemistry, 44, 13163-13171. Kinetic and Structural Analysis of Active Site Mutants of Monofunctional NAD-Dependent 5,10-Methylenetetrahydrofolate Dehydrogenase fromSaccharomyces cerevisiae†. DOI:10.1021/bi051038x. PMID:16185084.
  4. Sundararajan S et al. (2002), J Biol Chem, 277, 18703-18709. Residues Involved in the Mechanism of the Bifunctional Methylenetetrahydrofolate Dehydrogenase-Cyclohydrolase. THE ROLES OF GLUTAMINE 100 AND ASPARTATE 125. DOI:10.1074/jbc.m200127200. PMID:11904299.
  5. Allaire M et al. (1998), Structure, 6, 173-182. The 3-D structure of a folate-dependent dehydrogenase/cyclohydrolase bifunctional enzyme at 1.5 å resolution. DOI:10.1016/s0969-2126(98)00019-7. PMID:9519408.

Step 1.

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Catalytic Residues Roles

Residue Roles
Lys56A activator
Asp125A electrostatic stabiliser
Gln100A activator

Chemical Components

Step 1.

Contributors

James W. Murray, Gemma L. Holliday, Craig Porter