PDBsum entry 4h5e

Transferase/transferase inhibitor

PDB id: 4h5e

Contents

Protein chain

346 a.a.

Ligands

YS4

IPR

Metals

_MG ×3

Waters ×108

PDB id:

4h5e

Name:

Transferase/transferase inhibitor

Title:

Crystal structure of human fpps in ternary complex with ys0470 and isopentenyl pyrophosphate

Structure:

Farnesyl pyrophosphate synthase. Chain: f. Fragment: unp residues 67-419. Synonym: fpp synthase, fps, (2e,6e)-farnesyl diphosphate synthase, dimethylallyltranstransferase, farnesyl diphosphate synthase, geranyltranstransferase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: fdps, fps, kiaa1293. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.04Å R-factor: 0.188 R-free: 0.233

Authors:

J.Park,Y.-S.Lin,Y.S.Tsantrizos,A.M.Berghuis

Key ref:

J.Park et al. (2012). Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme's active site closure. Bmc Struct Biol, 12, 32. PubMed id: 23234314

Date:

18-Sep-12 Release date: 26-Dec-12

Protein chain

P14324  (FPPS_HUMAN) -  Farnesyl pyrophosphate synthase from Homo sapiens

Seq: 419 a.a.

Struc: 346 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.5.1.1 - dimethylallyltranstransferase.
• Pathway: Terpenoid biosynthesis
• Reaction: isopentenyl diphosphate + dimethylallyl diphosphate = (2E)- geranyl diphosphate + diphosphate

isopentenyl diphosphate (Bound ligand (Het Group name = IPR) corresponds exactly) + dimethylallyl diphosphate = (2E)- geranyl diphosphate + diphosphate

• Enzyme class 2: E.C.2.5.1.10 - (2E,6E)-farnesyl diphosphate synthase.

Pathway:

• Reaction: isopentenyl diphosphate + (2E)-geranyl diphosphate = (2E,6E)-farnesyl diphosphate + diphosphate

isopentenyl diphosphate + (2E)-geranyl diphosphate (Bound ligand (Het Group name = IPR) corresponds exactly) = (2E,6E)-farnesyl diphosphate + diphosphate

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

Bmc Struct Biol 12:32 (2012)

PubMed id: 23234314

Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme's active site closure.

J.Park, Y.S.Lin, J.W.De Schutter, Y.S.Tsantrizos, A.M.Berghuis.

ABSTRACT

ABSTRACT: BACKGROUND: Human farnesyl pyrophosphate synthase (FPPS) controls intracellular levels of farnesyl pyrophosphate, which is essential for various biological processes. Bisphosphonate inhibitors of human FPPS are valuable therapeutics for the treatment of bone-resorption disorders and have also demonstrated efficacy in multiple tumor types. Inhibition of human FPPS by bisphosphonates in vivo is thought to involve closing of the enzyme's C-terminal tail induced by the binding of the second substrate isopentenyl pyrophosphate (IPP). This conformational change, which occurs through a yet unclear mechanism, seals off the enzyme's active site from the solvent environment and is essential for catalysis. The crystal structure of human FPPS in complex with a novel bisphosphonate YS0470 and in the absence of a second substrate showed partial ordering of the tail in the closed conformation. RESULTS: We have determined crystal structures of human FPPS in ternary complex with YS0470 and the secondary ligands inorganic phosphate (Pi), inorganic pyrophosphate (PPi), and IPP. Binding of PPi or IPP to the enzyme-inhibitor complex, but not that of Pi, resulted in full ordering of the C-terminal tail, which is most notably characterized by the anchoring of R351 side chain to the main frame of the enzyme. Isothermal titration calorimetry experiments demonstrated that PPi binds more tightly to the enzyme-inhibitor complex than IPP, and differential scanning fluorometry experiments confirmed that Pi binding does not induce the tail ordering. Structure analysis identified a cascade of conformational changes required for the C-terminal tail rigidification involving Y349, F238, and Q242. The residues K57 and N59 upon PPi/IPP binding undergo subtler conformational changes, which may initiate this cascade. CONCLUSIONS: In human FPPS, Y349 functions as a safety switch that prevents any futile C-terminal closure and is locked in the "off" position in the absence of bound IPP. Q242 plays the role of a gatekeeper and directly controls the anchoring of R351 side chain. The interactions between the residues K57 and N59 and those upstream and downstream of Y349 are likely responsible for the switch activation. The findings of this study can be exploited for structure-guided optimization of existing inhibitors as well as development of new pharmacophores.