PDBsum entry 4gtc

Transferase

PDB id: 4gtc

Contents

Protein chains

218 a.a.

Ligands

FAD ×4

Waters ×266

PDB id:

4gtc

Name:

Transferase

Title:

T. Maritima fdts (e144r mutant) plus fad

Structure:

Thymidylate synthase thyx. Chain: a, b, c, d. Synonym: ts, tsase. Engineered: yes. Mutation: yes

Source:

Thermotoga maritima. Organism_taxid: 243274. Strain: atcc 43589 / msb8 / dsm 3109 / jcm 10099. Gene: thyx, thy1, tm_0449. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.97Å R-factor: 0.195 R-free: 0.236

Authors:

I.I.Mathews,S.A.Lesley,A.Kohen,A.Prabhakar

Key ref:

E.M.Koehn et al. (2012). Folate binding site of flavin-dependent thymidylate synthase. Proc Natl Acad Sci U S A, 109, 15722-15727. PubMed id: 23019356

Date:

28-Aug-12 Release date: 17-Oct-12

Protein chains

Q9WYT0  (THYX_THEMA) -  Flavin-dependent thymidylate synthase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 220 a.a.

Struc: 218 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.1.1.148 - thymidylate synthase (FAD).
• Reaction: dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADPH + H⁺ = dTMP + (6S)-5,6,7,8-tetrahydrofolate + NADP⁺

dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADPH + H(+) (Bound ligand (Het Group name = FAD) matches with 72.92% similarity) = dTMP + (6S)-5,6,7,8-tetrahydrofolate + NADP(+)

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

reference

Proc Natl Acad Sci U S A 109:15722-15727 (2012)

PubMed id: 23019356

Folate binding site of flavin-dependent thymidylate synthase.

E.M.Koehn, L.L.Perissinotti, S.Moghram, A.Prabhakar, S.A.Lesley, I.I.Mathews, A.Kohen.

ABSTRACT

The DNA nucleotide thymidylate is synthesized by the enzyme thymidylate synthase, which catalyzes the reductive methylation of deoxyuridylate using the cofactor methylene-tetrahydrofolate (CH(2)H(4)folate). Most organisms, including humans, rely on the thyA- or TYMS-encoded classic thymidylate synthase, whereas, certain microorganisms, including all Rickettsia and other pathogens, use an alternative thyX-encoded flavin-dependent thymidylate synthase (FDTS). Although several crystal structures of FDTSs have been reported, the absence of a structure with folates limits understanding of the molecular mechanism and the scope of drug design for these enzymes. Here we present X-ray crystal structures of FDTS with several folate derivatives, which together with mutagenesis, kinetic analysis, and computer modeling shed light on the cofactor binding and function. The unique structural data will likely facilitate further elucidation of FDTSs' mechanism and the design of structure-based inhibitors as potential leads to new antimicrobial drugs.