PDBsum entry 4l6h

Transferase

PDB id: 4l6h

Contents

Protein chain

761 a.a.

Ligands

HCS

MTX

Metals

_ZN

Waters ×646

PDB id:

4l6h

Name:

Transferase

Title:

Crystal structure of the candida albicans methionine synthase in complex with methotrexate and homocysteine

Structure:

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase. Chain: a. Synonym: cobalamin-independent methionine synthase, methionine synthase, vitamin-b12 independent isozyme. Engineered: yes. Mutation: yes

Source:

Candida albicans sc5314. Organism_taxid: 237561. Strain: bwp17. Gene: cao19.10083, cao19.2551, met6. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.75Å R-factor: 0.192 R-free: 0.235

Authors:

D.Ubhi,J.D.Robertus

Key ref:

D.Ubhi et al. (2014). Structural analysis of a fungal methionine synthase with substrates and inhibitors. J Mol Biol, 426, 1839-1847. PubMed id: 24524835 DOI: 10.1016/j.jmb.2014.02.006

Date:

12-Jun-13 Release date: 05-Mar-14

Protein chain

P82610  (METE_CANAL) -  5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase from Candida albicans (strain SC5314 / ATCC MYA-2876)

Seq: 767 a.a.

Struc: 761 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.1.1.14 - 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase.
• Reaction: 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = tetrahydropteroyltri-L-glutamate + L-methionine

5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine (Bound ligand (Het Group name = HCS) corresponds exactly) = tetrahydropteroyltri-L-glutamate + L-methionine (Bound ligand (Het Group name = MTX) matches with 56.60% similarity)

• Cofactor: Zn(2+)

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

reference

DOI no: 10.1016/j.jmb.2014.02.006

J Mol Biol 426:1839-1847 (2014)

PubMed id: 24524835

Structural analysis of a fungal methionine synthase with substrates and inhibitors.

D.Ubhi, G.Kago, A.F.Monzingo, J.D.Robertus.

ABSTRACT

The cobalamin-independent methionine synthase from Candida albicans, known as Met6p, is a 90-kDa enzyme that consists of two (βα)8 barrels. The active site is located between the two domains and has binding sites for a zinc ion and substrates l-homocysteine and 5-methyl-tetrahydrofolate-glutamate3. Met6p catalyzes transfer of the methyl group of 5-methyl-tetrahydrofolate-glutamate3 to the l-homocysteine thiolate to generate methionine. Met6p is essential for fungal growth, and we currently pursue it as an antifungal drug design target. Here we report the binding of l-homocysteine, methionine, and several folate analogs. We show that binding of l-homocysteine or methionine results in conformational rearrangements at the amino acid binding pocket, moving the catalytic zinc into position to activate the thiol group. We also map the folate binding pocket and identify specific binding residues, like Asn126, whose mutation eliminates catalytic activity. We also report the development of a robust fluorescence-based activity assay suitable for high-throughput screening. We use this assay and an X-ray structure to characterize methotrexate as a weak inhibitor of fungal Met6p.