PDBsum entry 1bk4

Hydrolase

PDB id: 1bk4

Contents

Protein chain

314 a.a. *

Ligands

SO4 ×2

Metals

_MG

Waters ×86

* Residue conservation analysis

PDB id:

1bk4

Name:

Hydrolase

Title:

Crystal structure of rabbit liver fructose-1,6-bisphosphatase at 2.3 angstrom resolution

Structure:

Protein (fructose-1,6-bisphosphatase). Chain: a. Synonym: fructose-1,6-diphosphatase. Ec: 3.1.3.11

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Organ: liver

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.30Å R-factor: 0.177

Authors:

D.Ghosh,C.M.Weeks,M.Erman,A.W.Roszak,R.Kaiser,H.Jornvall

Key ref:

C.M.Weeks et al. (1999). Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 A resolution. Acta Crystallogr D Biol Crystallogr, 55, 93. PubMed id: 10089399 DOI: 10.1107/S0907444998008750

Date:

14-Jul-98 Release date: 22-Jul-98

Protein chain

P00637  (F16P1_RABIT) -  Fructose-1,6-bisphosphatase 1 from Oryctolagus cuniculus

Seq: 338 a.a.

Struc: 314 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

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

reference

DOI no: 10.1107/S0907444998008750

Acta Crystallogr D Biol Crystallogr 55:93 (1999)

PubMed id: 10089399

Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 A resolution.

C.M.Weeks, A.W.Roszak, M.Erman, R.Kaiser, H.Jörnvall, D.Ghosh.

ABSTRACT

The three-dimensional structure of the R form of rabbit liver fructose 1,6-bisphosphatase (Fru-1,6-Pase; E.C. 3.1.3.11) has been determined by a combination of heavy-atom and molecular-replacement methods. A model, which includes 2394 protein atoms and 86 water molecules, has been refined at 2.3 A resolution to a crystallographic R factor of 0.177. The root-mean-square deviations of bond distances and angles from standard geometry are 0.012 A and 1.7 degrees, respectively. This structural result, in conjunction with recently redetermined amino-acid sequence data, unequivocally establishes that the rabbit liver enzyme is not an aberrant bisphosphatase as once believed, but is indeed homologous to other Fru-1,6-Pases. The root-mean-square deviation of the Calpha atoms in the rabbit liver structure from the homologous atoms in the pig kidney structure complexed with the product, fructose 6-phosphate, is 0.7 A. Fru-1,6-Pases are homotetramers, and the rabbit liver protein crystallizes in space group I222 with one monomer in the asymmetric unit. The structure contains a single endogenous Mg2+ ion coordinated by Glu97, Asp118, Asp121 and Glu280 at the site designated metal site 1 in pig kidney Fru-1,6-Pase R-form complexes. In addition, two sulfate ions, which are found at the positions normally occupied by the 6-phosphate group of the substrate, as well as the phosphate of the allosteric inhibitor AMP appear to provide stability. Met177, which has hydrophobic contacts with the adenine moiety of AMP in pig kidney T-form complexes, is replaced by glycine. Binding of a non-hydrolyzable substrate analog, beta-methyl-fructose 1,6-bisphosphate, at the catalytic site is also examined.

Selected figure(s)

Figure 6.
Figure 6 Coordination of the sulfate ion at the site occupied by the 6-phosphate group of pig kidney enzyme complexes with product, competitive inhibitor, substrate and substrate analogs. Hydrogen-bond distances 3.2 Å are indicated.

Figure 7.
Figure 7 Coordination of the sulfate ion at the site occupied by the phosphate moiety of AMP in the pig kidney enzyme complexes. Hydrogen-bond distances 3.2 Å are indicated.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 93-0) copyright 1999.

Figures were selected by an automated process.