PDBsum entry 2flo

Hydrolase

PDB id: 2flo

Contents

Protein chains

496 a.a. *

Waters ×630

* Residue conservation analysis

PDB id:

2flo

Name:

Hydrolase

Title:

Crystal structure of exopolyphosphatase (ppx) from e. Coli o157:h7

Structure:

Exopolyphosphatase. Chain: a, b, c, d. Synonym: exopolypase, metaphosphatase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83334. Strain: o157:h7. Gene: ppx. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.205 R-free: 0.247

Authors:

E.S.Rangarajan,M.Cygler,A.Matte,Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)

Key ref:

E.S.Rangarajan et al. (2006). The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains. J Mol Biol, 359, 1249-1260. PubMed id: 16678853 DOI: 10.1016/j.jmb.2006.04.031

Date:

06-Jan-06 Release date: 06-Jun-06

Protein chains

P0AFL8  (PPX_ECO57) -  Exopolyphosphatase from Escherichia coli O157:H7

Seq: 513 a.a.

Struc: 496 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.11 - exopolyphosphatase.
• Reaction: [phosphate](n) + H2O = [phosphate](n-1) + phosphate + H⁺

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

Key reference

DOI no: 10.1016/j.jmb.2006.04.031

J Mol Biol 359:1249-1260 (2006)

PubMed id: 16678853

The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains.

E.S.Rangarajan, G.Nadeau, Y.Li, J.Wagner, M.N.Hung, J.D.Schrag, M.Cygler, A.Matte.

ABSTRACT

Polyphosphate (polyP) is a linear polymer consisting of tens to hundreds of phosphate molecules joined together by high-energy anhydride bonds. These polymers are found in virtually all prokaryotic and eukaryotic cells and perform many functions; prominent among them are the responses to many stresses. Polyphosphate is synthesized by polyP kinase (PPK), using the terminal phosphate of ATP as the substrate, and degraded to inorganic phosphate by both endo- and exopolyphosphatases. Here we report the crystal structure and analysis of the polyphosphate phosphatase PPX from Escherichia coli O157:H7 refined at 2.2 Angstroms resolution. PPX is made of four domains. Domains I and II display structural similarity with one another and share the ribonuclease-H-like fold. Domain III bears structural similarity to the N-terminal, HD domain of SpoT. Domain IV, the smallest domain, has structural counterparts in cold-shock associated RNA-binding proteins but is of unknown function in PPX. The putative PPX active site is located at the interface between domains I and II. In the crystal structure of PPX these two domains are close together and represent the "closed" state. Comparison with the crystal structure of PPX/GPPA from Aquifex aeolicus reveals close structural similarity between domains I and II of the two enzymes, with the PPX/GPPA representing an "open" state. A striking feature of the dimer is a deep S-shaped canyon extending along the dimer interface and lined with positively charged residues. The active site region opens to this canyon. We postulate that this is a likely site of polyP binding.

Selected figure(s)

Figure 4.
Figure 4. Comparison of the metal-binding sites of E. coli PPX (dark grey) and PPX/GPPA from A. aeolicus (light grey). The residue pairs Asp141/Asp143, Ser146/Ser148 and Glu148/Glu150 were used to generate the superposition.

Figure 6.
Figure 6. (a) Putative active site region of E. coli PPX located at the interface of domains I and II. The pertinent residues are shown in stick representation. Surface representation of the interface between domains I and II in (b) E. coli PPX (closed state) and (c) A. aeolicus PPX/GPPA (open state). Both molecules are shown in the same orientation and were first superposed as in Figure 3. Domain colors are as in Figure 1, with highly conserved residues shown in yellow.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 1249-1260) copyright 2006.

Figures were selected by an automated process.