PDBsum entry 1njs

Transferase

PDB id: 1njs

Contents

Protein chains

200 a.a. *

Ligands

PO4 ×3

KEU ×2

Waters ×251

* Residue conservation analysis

PDB id:

1njs

Name:

Transferase

Title:

Human gar tfase in complex with hydrolyzed form of 10-trifluoroacetyl- 5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid

Structure:

Phosphoribosylglycinamide formyltransferase. Chain: a, b. Synonym: gar tfase, gart, gar transformylase, 5'- phosphoribosylglycinamide transformylase. Engineered: yes

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

1.98Å R-factor: 0.228 R-free: 0.247

Authors:

Y.Zhang,J.Desharnais,T.H.Marsilje,C.Li,M.P.Hedrick,L.T.Gooljarsingh, A.Tavassoli,S.J.Benkovic,A.J.Olson,D.L.Boger,I.A.Wilson

Key ref:

Y.Zhang et al. (2003). Rational design, synthesis, evaluation, and crystal structure of a potent inhibitor of human GAR Tfase: 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid. Biochemistry, 42, 6043-6056. PubMed id: 12755606 DOI: 10.1021/bi034219c

Date:

02-Jan-03 Release date: 10-Jun-03

Protein chains

P22102  (PUR2_HUMAN) -  Trifunctional purine biosynthetic protein adenosine-3 from Homo sapiens

Seq: 1010 a.a.

Struc: 200 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.1.2.2 - phosphoribosylglycinamide formyltransferase 1.
• Pathway: Purine Biosynthesis (early stages)
• Reaction: N₁-(5-phospho-beta-D-ribosyl)glycinamide + (6R)-10- formyltetrahydrofolate = N₂-formyl-N₁-(5-phospho-beta-D- ribosyl)glycinamide + (6S)-5,6,7,8-tetrahydrofolate + H⁺
• Enzyme class 2: E.C.6.3.3.1 - phosphoribosylformylglycinamidine cyclo-ligase.

Pathway:

• Reaction: 2-formamido-N₁-(5-O-phospho-beta-D-ribosyl)acetamidine + ATP = 5-amino- 1-(5-phospho-beta-D-ribosyl)imidazole + ADP + phosphate + H⁺

2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ATP = 5-amino- 1-(5-phospho-beta-D-ribosyl)imidazole + ADP + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

• Cofactor: Magnesium
• Enzyme class 3: E.C.6.3.4.13 - phosphoribosylamine--glycine ligase.

Pathway:

• Reaction: 5-phospho-beta-D-ribosylamine + glycine + ATP = N₁-(5-phospho-beta-D- ribosyl)glycinamide + ADP + phosphate + H⁺

5-phospho-beta-D-ribosylamine + glycine + ATP = N(1)-(5-phospho-beta-D- ribosyl)glycinamide + ADP + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

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/bi034219c

Biochemistry 42:6043-6056 (2003)

PubMed id: 12755606

Rational design, synthesis, evaluation, and crystal structure of a potent inhibitor of human GAR Tfase: 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid.

Y.Zhang, J.Desharnais, T.H.Marsilje, C.Li, M.P.Hedrick, L.T.Gooljarsingh, A.Tavassoli, S.J.Benkovic, A.J.Olson, D.L.Boger, I.A.Wilson.

ABSTRACT

Glycinamide ribonucleotide transformylase (GAR Tfase) has been the target of anti-neoplastic intervention for almost two decades. Here, we use a structure-based approach to design a novel folate analogue, 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid (10-CF(3)CO-DDACTHF, 1), which specifically inhibits recombinant human GAR Tfase (K(i) = 15 nM), but is inactive (K(i) > 100 microM) against other folate-dependent enzymes that have been examined. Moreover, compound 1 is a potent inhibitor of tumor cell proliferation (IC(50) = 16 nM, CCRF-CEM), which represents a 10-fold improvement over Lometrexol, a GAR Tfase inhibitor that has been in clinical trials. Thus, this folate analogue 1 is among the most potent and selective inhibitors known toward GAR Tfase. Contributing to its efficacious activity, compound 1 is effectively transported into the cell by the reduced folate carrier and intracellularly sequestered by polyglutamation. The crystal structure of human GAR Tfase with folate analogue 1 at 1.98 A resolution represents the first structure of any GAR Tfase to be determined with a cofactor or cofactor analogue without the presence of substrate. The folate-binding loop of residues 141-146, which is highly flexible in both Escherichia coli and unliganded human GAR Tfase structures, becomes highly ordered upon binding 1 in the folate-binding site. Computational docking of the natural cofactor into this and other apo or complexed structures provides a rational basis for modeling how the natural cofactor 10-formyltetrahydrofolic acid interacts with GAR Tfase, and suggests that this folate analogue-bound conformation represents the best template to date for inhibitor design.