Methenyltetrahydrofolate cyclohydrolase

 

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 has two active sites: the bifunctional enzyme methylenetetrahydrofolate dehydrogenase – cyclohydrolase catalyses two sequential reactions involved in the interconversion of substituted tetrahydrofolates. The interconversion of 5,10-methylene-H4folate with 5,10-methenyl-H4folate is accomplished through the NADP+-dependent dehydrogenase activity, whereas 5,10-methenyl-H4folate and 10-formyl-H4folate are interconverted by the cyclohydrolase activity. The second domain represents the formate-tetrahydrofolate ligase (EC 6.3.4.3) 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). This entry represents the bifunctional activity.

 

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:3.5.4.9)

NADP(3-)
CHEBI:58349ChEBI
+
(6R)-5,10-methylenetetrahydrofolic acid
CHEBI:1989ChEBI
+
water
CHEBI:15377ChEBI
→
NADPH(4-)
CHEBI:57783ChEBI
+
10-formyltetrahydrofolate(2-)
CHEBI:57454ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: Citrovorum factor cyclodehydrase, Cyclohydrolase, Formyl-methenyl-methylenetetrahydrofolate synthetase (combined), 5,10-methenyltetrahydrofolate 5-hydrolase (decyclizing),

Enzyme Mechanism

Introduction

In the first half-reaction, which relates to EC number 1.5.1.5, a hydride is eliminated from the THF substrate. In the same active site, the second half reaction, which relates to EC number 3.5.4.9. In this hydrolysis reaction, a water molecule, positioned by Gln100 and activated by Lys56, attacks the substrate. It is then deprotonated by Lys56, which transfers the proton to elsewhere on the substrate. Lys56 then deprotonates the newly formed alcohol group on the intermediate, causing it to be reduced to a ketone and break open one of the rings in the substrate. Lys56 is restored to its original state by protonating a water molecule.

Catalytic Residues Roles

UniProt PDB* (1a4i)
*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. 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.
  4. Bartoschek S et al. (2001), Chembiochem, 2, 530-541. Re-face stereospecificity of methylenetetrahydromethanopterin and methylenetetrahydrofolate dehydrogenases is predetermined by intrinsic properties of the substrate. PMID:11828486.
  5. Monzingo AF et al. (2000), Protein Sci, 9, 1374-1381. The X-ray structure of the NAD-dependent 5,10-methylenetetrahydrofolate dehydrogenase fromSaccharomyces cerevisiae. DOI:10.1110/ps.9.7.1374. PMID:10933503.
  6. Shen BW et al. (1999), Protein Sci, 8, 1342-1349. The crystal structure of a bacterial, bifunctional 5, 10 methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. DOI:10.1110/ps.8.6.1342. PMID:10386884.
  7. 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 proton shuttle (general acid/base)
Gln100A activator
Ser49A activator

Chemical Components

Step 1.

Contributors

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