PDBsum entry 1q9d

Hydrolase

PDB id: 1q9d

Contents

Protein chains

328 a.a. *

Ligands

F6P ×2

PO4 ×4

OI1 ×2

Metals

_MG ×4

Waters ×291

* Residue conservation analysis

PDB id:

1q9d

Name:

Hydrolase

Title:

Fructose-1,6-bisphosphatase complexed with a new allosteric site inhibitor (i-state)

Structure:

Fructose-1,6-bisphosphatase. Chain: a, b. Synonym: d-fructose-1,6-bisphosphate 1-phosphohydrolase, fbpase. Engineered: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Tissue: liver. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.35Å R-factor: 0.191 R-free: 0.246

Authors:

R.B.Honzatko,J.Y.Choe

Key ref:

J.Y.Choe et al. (2003). Inhibition of fructose-1,6-bisphosphatase by a new class of allosteric effectors. J Biol Chem, 278, 51176-51183. PubMed id: 14530289 DOI: 10.1074/jbc.M308396200

Date:

25-Aug-03 Release date: 02-Dec-03

Protein chains

P00636  (F16P1_PIG) -  Fructose-1,6-bisphosphatase 1 from Sus scrofa

Seq: 338 a.a.

Struc: 328 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.3.11 - fructose-bisphosphatase.
• Pathway: Pentose Phosphate Pathway (later stages)
• Reaction: beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate

beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate (Bound ligand (Het Group name = F6P) corresponds exactly) + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

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

reference

DOI no: 10.1074/jbc.M308396200

J Biol Chem 278:51176-51183 (2003)

PubMed id: 14530289

Inhibition of fructose-1,6-bisphosphatase by a new class of allosteric effectors.

J.Y.Choe, S.W.Nelson, K.L.Arienti, F.U.Axe, T.L.Collins, T.K.Jones, R.D.Kimmich, M.J.Newman, K.Norvell, W.C.Ripka, S.J.Romano, K.M.Short, D.H.Slee, H.J.Fromm, R.B.Honzatko.

ABSTRACT

A highly constrained pseudo-tetrapeptide (OC252-324) further defines a new allosteric binding site located near the center of fructose-1,6-bisphosphatase. In a crystal structure, pairs of inhibitory molecules bind to opposite faces of the enzyme tetramer. Each ligand molecule is in contact with three of four subunits of the tetramer, hydrogen bonding with the side chain of Asp187 and the backbone carbonyl of residue 71, and electrostatically interacting with the backbone carbonyl of residue 51. The ligated complex adopts a quaternary structure between the canonical R- and T-states of fructose-1,6-bisphosphatase, and yet a dynamic loop essential for catalysis (residues 52-72) is in a conformation identical to that of the T-state enzyme. Inhibition by the pseudo-tetrapeptide is cooperative (Hill coefficient of 2), synergistic with both AMP and fructose 2,6-bisphosphate, noncompetitive with respect to Mg2+, and uncompetitive with respect to fructose 1,6-bisphosphate. The ligand dramatically lowers the concentration at which substrate inhibition dominates the kinetics of fructose-1,6-bisphosphatase. Elevated substrate concentrations employed in kinetic screens may have facilitated the discovery of this uncompetitive inhibitor. Moreover, the inhibitor could mimic an unknown natural effector of fructose-1,6-bisphosphatase, as it interacts strongly with a conserved residue of undetermined functional significance.

Selected figure(s)

Figure 3.
FIG. 3. Kinetic mechanism of inhibition of FBPase by OC252. A, data are taken at 1-20 µM F16P[2] in 50 mM Hepes, pH 7.5, with 5 mM MgCl[2]. Curves are fits to the data using Equation 3. B, data are taken at 0.1-5 mM Mg2+ (corrected for chelation by EDTA) in 50 mM Hepes, pH 7.5, with 20 µM F16P[2]. Curves are fits to the data using Equation 4.

Figure 4.
FIG. 4. OC252-FBPase complex. The top panel gives orthogonal views of the complex showing FBPase as a ribbon with atoms of Mg2+, F6P, P[i], and OC252 as spheres. The bottom panel shows electron density covering a pair of OC252 molecules from an omit map contoured at a level of 1 with a cut-off radius of 1 Å (bottom). This drawing was prepared with MOLSCRIPT (41).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 51176-51183) copyright 2003.

Figures were selected by an automated process.