PDBsum entry 1dib

Oxidoreductase,hydrolase

PDB id: 1dib

Contents

Protein chains

285 a.a. *

Ligands

NAP ×2

L34

Waters ×110

* Residue conservation analysis

PDB id:

1dib

Name:

Oxidoreductase,hydrolase

Title:

Human methylenetetrahydrofolate dehydrogenase / cyclohydrolase complexed with NADP and inhibitor ly345899

Structure:

Methylenetetrahydrofolate dehydrogenase/cyclohydrolase. Chain: a, b. Synonym: dc301. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.208 R-free: 0.240

Authors:

A.Schmidt,H.Wu,R.E.Mackenzie,V.J.Chen,J.R.Bewly,J.E.Ray,J.E.Toth, M.Cygler

Key ref:

A.Schmidt et al. (2000). Structures of three inhibitor complexes provide insight into the reaction mechanism of the human methylenetetrahydrofolate dehydrogenase/cyclohydrolase. Biochemistry, 39, 6325-6335. PubMed id: 10828945 DOI: 10.1021/bi992734y

Date:

29-Nov-99 Release date: 05-Jul-00

Protein chains

P11586  (C1TC_HUMAN) -  C-1-tetrahydrofolate synthase, cytoplasmic from Homo sapiens

Seq: 935 a.a.

Struc: 285 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: E.C.1.5.1.5 - methylenetetrahydrofolate dehydrogenase (NADP(+)).
• Pathway: Folate Coenzymes
• Reaction: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP⁺ = (6R)-5,10- methenyltetrahydrofolate + NADPH

(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = (6R)-5,10- methenyltetrahydrofolate + NADPH

• Enzyme class 2: E.C.3.5.4.9 - methenyltetrahydrofolate cyclohydrolase.

Pathway:

• Reaction: (6R)-5,10-methenyltetrahydrofolate + H2O = (6R)-10-formyltetrahydrofolate + H⁺
• Enzyme class 3: E.C.6.3.4.3 - formate--tetrahydrofolate ligase.

Pathway:

• Reaction: (6S)-5,6,7,8-tetrahydrofolate + formate + ATP = (6R)-10- formyltetrahydrofolate + ADP + phosphate

(6S)-5,6,7,8-tetrahydrofolate + formate + ATP = (6R)-10- formyltetrahydrofolate + ADP (Bound ligand (Het Group name = NAP) matches with 56.25% similarity) + phosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi992734y

Biochemistry 39:6325-6335 (2000)

PubMed id: 10828945

Structures of three inhibitor complexes provide insight into the reaction mechanism of the human methylenetetrahydrofolate dehydrogenase/cyclohydrolase.

A.Schmidt, H.Wu, R.E.MacKenzie, V.J.Chen, J.R.Bewly, J.E.Ray, J.E.Toth, M.Cygler.

ABSTRACT

Enzymes involved in tetrahydrofolate metabolism are of particular pharmaceutical interest, as their function is crucial for amino acid and DNA biosynthesis. The crystal structure of the human cytosolic methylenetetrahydrofolate dehydrogenase/cyclohydrolase (DC301) domain of a trifunctional enzyme has been determined previously with a bound NADP cofactor. While the substrate binding site was identified to be localized in a deep and rather hydrophobic cleft at the interface between two protein domains, the unambiguous assignment of catalytic residues was not possible. We succeeded in determining the crystal structures of three ternary DC301/NADP/inhibitor complexes. Investigation of these structures followed by site-directed mutagenesis studies allowed identification of the amino acids involved in catalysis by both enzyme activities. The inhibitors bind close to Lys56 and Tyr52, residues of a strictly conserved motif for active sites in dehydrogenases. While Lys56 is in a good position for chemical interaction with the substrate analogue, Tyr52 was found stacking against the inhibitors' aromatic rings and hence seems to be more important for proper positioning of the ligand than for catalysis. Also, Ser49 and/or Cys147 were found to possibly act as an activator for water in the cyclohydrolase step. These and the other residues (Gln100 and Asp125), with which contacts are made, are strictly conserved in THF dehydrogenases. On the basis of structural and mutagenesis data, we propose a reaction mechanism for both activities, the dehydrogenase and the cyclohydrolase.