PDBsum entry 2flo

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protein Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
496 a.a. *
Waters ×630
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of exopolyphosphatase (ppx) from e. Coli o
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)
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
06-Jan-06     Release date:   06-Jun-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0AFL8  (PPX_ECO57) -  Exopolyphosphatase
513 a.a.
496 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Exopolyphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (Polyphosphate)(n) + H2O = (polyphosphate)(n-1) + phosphate
+ H(2)O
= (polyphosphate)(n-1)
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     polyphosphate catabolic process   1 term 
  Biochemical function     hydrolase activity     3 terms  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19344251 N.N.Rao, M.R.Gómez-García, and A.Kornberg (2009).
Inorganic polyphosphate: essential for growth and survival.
  Annu Rev Biochem, 78, 605-647.  
19304823 S.N.Lindner, S.Knebel, H.Wesseling, S.M.Schoberth, and V.F.Wendisch (2009).
Exopolyphosphatases PPX1 and PPX2 from Corynebacterium glutamicum.
  Appl Environ Microbiol, 75, 3161-3170.  
18173655 J.Hegermann, H.Lünsdorf, J.Overbeck, and H.Schrempf (2008).
Polyphosphate at the Streptomyces lividans cytoplasmic membrane is enhanced in the presence of the potassium channel KcsA.
  J Microsc, 229, 174-182.  
18458329 M.Zebisch, and N.Sträter (2008).
Structural insight into signal conversion and inactivation by NTPDase2 in purinergic signaling.
  Proc Natl Acad Sci U S A, 105, 6882-6887.
PDB codes: 3cj1 3cj7 3cj9 3cja
18782773 R.Jain, and S.Shuman (2008).
Polyphosphatase Activity of CthTTM, a Bacterial Triphosphate Tunnel Metalloenzyme.
  J Biol Chem, 283, 31047-31057.  
17827150 J.Fang, F.A.Ruiz, M.Docampo, S.Luo, J.C.Rodrigues, L.S.Motta, P.Rohloff, and R.Docampo (2007).
Overexpression of a Zn2+-sensitive soluble exopolyphosphatase from Trypanosoma cruzi depletes polyphosphate and affects osmoregulation.
  J Biol Chem, 282, 32501-32510.  
17215253 M.Tammenkoski, V.M.Moiseev, M.Lahti, E.Ugochukwu, T.H.Brondijk, S.A.White, R.Lahti, and A.A.Baykov (2007).
Kinetic and mutational analyses of the major cytosolic exopolyphosphatase from Saccharomyces cerevisiae.
  J Biol Chem, 282, 9302-9311.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.