PDBsum entry: 1ipw

Hydrolase

PDB id: 1ipw

Contents

Protein chains

168 a.a. *

Metals

_MG ×3

Waters ×111

* Residue conservation analysis

PDB id:

1ipw

Name:

Hydrolase

Title:

Inorganic pyrophosphatase from escherichia coli with three m ions

Structure:

Soluble inorganic pyrophosphatase. Chain: a, b. Ec: 3.6.1.1

Source:

Escherichia coli. Organism_taxid: 562

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.30Å R-factor: 0.171 R-free: 0.239

Authors:

J.A.Kankare,A.Goldman

Key ref:

J.Kankare et al. (1996). Crystallographic identification of metal-binding sites in Escherichia coli inorganic pyrophosphatase. Biochemistry, 35, 4670-4677. PubMed id: 8664256 DOI: 10.1021/bi952637e

Date:

04-Mar-96 Release date: 20-Aug-97

Protein chains

P0A7A9  (IPYR_ECOLI) -  Inorganic pyrophosphatase

Seq: 176 a.a.

Struc: 168 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.1 - Inorganic diphosphatase.
• Reaction: Diphosphate + H₂O = 2 phosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (3 terms)
• Biological process: phosphate metabolic process (1 term)
• Biochemical function: hydrolase activity (5 terms)

Added reference

DOI no: 10.1021/bi952637e

Biochemistry 35:4670-4677 (1996)

PubMed id: 8664256

Crystallographic identification of metal-binding sites in Escherichia coli inorganic pyrophosphatase.

J.Kankare, T.Salminen, R.Lahti, B.S.Cooperman, A.A.Baykov, A.Goldman.

ABSTRACT

We report refined crystal structures of the hexameric soluble inorganic pyrophosphatase from Escherichia coli (E-PPase) to R-factors of 18.3% and 17.1% at 2.2 and 2.3 angstroms, respectively. Both structures contain two independent monomers in the asymmetric unit of an R32 cell. The difference between the structures is that the latter contains 1.5 Mg2+ ions per monomer. One metal ion binds to the "tight" metal-binding site identified by equilibrium dialysis studies, and is coordinated to Asp65, Asp70, and Asp102. The other metal ion, shared between two monomers at a hitherto unidentified metal-binding site in the dyad interface between trimers, is coordinated through water molecules to Asp26s and Asn24s from two monomers. The hexamers with metal bound to them are more tightly associated than the ones without metal bound to them. Combined with our other mechanistic and structural data, the results suggest that, at high metal concentrations, E-PPase may bind at least 4.5 metals per monomer: two in the active site before binding substrate, two with substrate, and 0.5 in the dyad interface. Glu20 interacts via a water molecule with Asp70 and appears in the related yeast PPase structure (Heikinheimo, manuscript in preparation) to be involved in binding the second metal ion. Magnesium ion therefore stabilizes the hexamer form through both direct and indirect effects. The direct effect is by tighter association at the subunit interface; the indirect effect occurs because magnesium stabilizes the correct conformation of the loop between Glu20 and Ile32, a loop involved a trimer-trimmer interactions. Our results thus provide a structural explanation for the solution studies that show that the E20D variant is partially hexameric and that the hexamer form can be stabilized by binding magnesium ion.