PDBsum entry 1nux

Hydrolase

PDB id: 1nux

Contents

Protein chain

328 a.a. *

Ligands

F6P

PO3

_MG ×3

Waters ×226

* Residue conservation analysis

PDB id:

1nux

Name:

Hydrolase

Title:

Fructose-1,6-bisphosphatase complex with magnesium, fructose-6- phosphate, phosphate and inhibitory concentrations of potassium (200mm)

Structure:

Fructose-1,6-bisphosphatase. Chain: a. Engineered: yes

Source:

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

Biol. unit:

Tetramer (from PQS)

Resolution:

1.60Å R-factor: 0.158 R-free: 0.208

Authors:

J.Choe,C.V.Iancu,H.J.Fromm,R.B.Honzatko

Key ref:

J.Y.Choe et al. (2003). Metaphosphate in the active site of fructose-1,6-bisphosphatase. J Biol Chem, 278, 16015-16020. PubMed id: 12595528 DOI: 10.1074/jbc.M212395200

Date:

01-Feb-03 Release date: 08-Jul-03

Protein chain

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 = PO3) matches with 80.00% similarity)

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

reference

DOI no: 10.1074/jbc.M212395200

J Biol Chem 278:16015-16020 (2003)

PubMed id: 12595528

Metaphosphate in the active site of fructose-1,6-bisphosphatase.

J.Y.Choe, C.V.Iancu, H.J.Fromm, R.B.Honzatko.

ABSTRACT

The hydrolysis of a phosphate ester can proceed through an intermediate of metaphosphate (dissociative mechanism) or through a trigonal bipryamidal transition state (associative mechanism). Model systems in solution support the dissociative pathway, whereas most enzymologists favor an associative mechanism for enzyme-catalyzed reactions. Crystals of fructose-1,6-bisphosphatase grow from an equilibrium mixture of substrates and products at near atomic resolution (1.3 A). At neutral pH, products of the reaction (orthophosphate and fructose 6-phosphate) bind to the active site in a manner consistent with an associative reaction pathway; however, in the presence of inhibitory concentrations of K+ (200 mm), or at pH 9.6, metaphosphate and water (or OH-) are in equilibrium with orthophosphate. Furthermore, one of the magnesium cations in the pH 9.6 complex resides in an alternative position, and suggests the possibility of metal cation migration as the 1-phosphoryl group of the substrate undergoes hydrolysis. To the best of our knowledge, the crystal structures reported here represent the first direct observation of metaphosphate in a condensed phase and may provide the structural basis for fundamental changes in the catalytic mechanism of fructose-1,6-bisphosphatase in response to pH and different metal cation activators.

Selected figure(s)

Figure 1.
Fig. 1. Stereoviews of FBPase active sites. A, complex of Mg2+, F6P, and orthophosphate at pH 7 (control complex). B, complex of Mg2+, K+/Zn2+, F6P, and metaphosphate at pH 7 (high K+ complex). C, complex of Mg2+, F6P, and metaphosphate at pH 9.6 (high pH complex). Electron density (blue) covers metaphosphate/hydroxide anions or orthophosphate at a contour level of 3 , using a cutoff radius of 1 Å. Anomalous difference density (red) covers site M1 at a contour level of 3 , using a cutoff radius of 1 Å. MOLSCRIPT (39) and RASTER3D (35) were used for the illustration.

Figure 2.
Fig. 2. Distance relations between selected atoms in the active site. A, control complex. B, high K+ complex. C, high pH complex. The dotted outline in panel C represents a channel of electron density that extends between metal sites 3 and 4, which in the refined model is represented by a discrete set of water molecules and magnesium cations.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 16015-16020) copyright 2003.

Figures were selected by an automated process.