PDBsum entry 2eip

Inorganic pyrophosphatase

PDB id: 2eip

Contents

Protein chains

168 a.a. *

173 a.a. *

Waters ×141

* Residue conservation analysis

PDB id:

2eip

Name:

Inorganic pyrophosphatase

Title:

Inorganic pyrophosphatase

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:

2.20Å R-factor: 0.183 R-free: 0.234

Authors:

J.A.Kankare,T.Salminen,A.Goldman

Key ref:

J.Kankare et al. (1996). Structure of Escherichia coli inorganic pyrophosphatase at 2.2 A resolution. Acta Crystallogr D Biol Crystallogr, 52, 551-563. PubMed id: 15299678 DOI: 10.1107/S0907444996000376

Date:

10-Jan-96 Release date: 08-Nov-96

Supersedes:

1eip

Protein chain

P0A7A9  (IPYR_ECOLI) -  Inorganic pyrophosphatase from Escherichia coli (strain K12)

Seq: 176 a.a.

Struc: 168 a.a.

Protein chain

P0A7A9  (IPYR_ECOLI) -  Inorganic pyrophosphatase from Escherichia coli (strain K12)

Seq: 176 a.a.

Struc: 173 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.6.1.1 - inorganic diphosphatase.
• Reaction: diphosphate + H2O = 2 phosphate + H⁺

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

Added reference

DOI no: 10.1107/S0907444996000376

Acta Crystallogr D Biol Crystallogr 52:551-563 (1996)

PubMed id: 15299678

Structure of Escherichia coli inorganic pyrophosphatase at 2.2 A resolution.

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

ABSTRACT

The refined crystal structures of hexameric soluble inorganic pyrophosphatase from E. coli (E-PPase) are reported to R factors of 18.7 and 18.3% at 2.15 and 2.2 A, respectively. The first contains one independent monomer; the other, two independent monomers, in an R32 unit cell. Because the E-PPase monomer is small with a large open active site, there are relatively few hydrophobic interactions that connect the active-site loops to the five-stranded twisted beta-barrel that is the hydrophobic core of the molecule. The active-site loops are, however, held in place by interactions between monomers around the threefold and twofold symmetry axes of the D(3) hexamer. Consequently, mutations of active-site residues (such as Glu20 and Lysl04) often affect protein stability and oligomeric structure. Conversely, mutations of residues in the interface between monomers (such as His136 and Hisl40) not only affect oligomeric structure but also affect active-site function. The effects of the H136Q and H140Q variants can be explained by the extended ionic interaction between H140, D143 and H136' of the neighbouring monomer. This interaction is further buttressed by an extensive hydrogen-bonding network that appears to explain why the E-PPase hexamer is so stable and also why the H136Q and H140Q variant proteins are less stable as hexamers.

Selected figure(s)

Figure 4.
Fig. 4. (a). A stereo diagram of the C~ trace of E. coli PPase showing the overall topology of the enzyme. The colouring scheme follows this definition: the barrel and the parts belonging to it are coloured green and the excursions red. The resi- dues belonging to the hydrophobic core of the barrel are blue and the residues which participate in inter- monomeric contacts are yellow. The missing loops in the short c-axis form and the long c-axis form monomer II are shown as dotted lines. This figure was drawn using MOLSCRIPT (Kraulis, 1991).

Figure 7.
Fig. 7. (a) Hydrophilic intratrimefic contacts between monomers related by the threefold axis sh6wn in a MOLSCRIPT (Kraulis, 1991) stereo diagram. Two adja- cent symmetry mates around the threefold axis are dark and light grey and hydrogen bonds are shown with dashed lines. The curved arrows pointing upwards is f12, the one pointing down is 133. (b) Hydrophobic intratrimeric con- tacts between monomers related by the threefold axis shown in a MOLSCRIPT (Kraulis, 1991 ) stereo diagram. Two adjacent sym- metry mates around the threefold axis are dark and light grey. The 'residues involved in hydrophobic interactions are marked. The view is approximately the same as in (a), but 'lower down' on the long fl2- /33 loop; in (a), the top of the loop can be seen.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 551-563) copyright 1996.

Figures were selected by an automated process.