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PDBsum entry 1u6z

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1u6z
Jmol
Contents
Protein chains
498 a.a. *
Ligands
SO4 ×29
Waters ×634
* Residue conservation analysis
PDB id:
1u6z
Name: Hydrolase
Title: Structure of an e. Coli exopolyphosphatase: insight into the processive hydrolysis of polyphosphate and its regulation
Structure: Exopolyphosphatase. Chain: a, b. Synonym: exopolypase, metaphosphatase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: ppx. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.208     R-free:   0.242
Authors: M.S.Hasson,J.Alvarado,D.A.Sanders
Key ref:
J.Alvarado et al. (2006). Origin of exopolyphosphatase processivity: Fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog. Structure, 14, 1263-1272. PubMed id: 16905100 DOI: 10.1016/j.str.2006.06.009
Date:
02-Aug-04     Release date:   06-Dec-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AFL6  (PPX_ECOLI) -  Exopolyphosphatase
Seq:
Struc:
513 a.a.
498 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.1.11  - Exopolyphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (Polyphosphate)(n) + H2O = (polyphosphate)(n-1) + phosphate
(Polyphosphate)(n)
+ 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  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2006.06.009 Structure 14:1263-1272 (2006)
PubMed id: 16905100  
 
 
Origin of exopolyphosphatase processivity: Fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog.
J.Alvarado, A.Ghosh, T.Janovitz, A.Jauregui, M.S.Hasson, D.A.Sanders.
 
  ABSTRACT  
 
The Escherichia coli Ppx protein is an exopolyphosphatase that degrades long-chain polyphosphates in a highly processive reaction. It also hydrolyzes the terminal 5' phosphate of the modified nucleotide guanosine 5' triphosphate 3' diphosphate (pppGpp). The structure of Ppx has been determined to 1.9 A resolution by X-ray crystallography. The exopolyphosphatase is an ASKHA (acetate and sugar kinases, Hsp70, actin) phosphotransferase with an active site found in a cleft between the two amino-terminal domains. Analysis of the active site indicates that among the ASKHA phosphotranferases of known structure, Ppx is the closest to the ectonucleoside triphosphate diphosphohydrolases. A third domain forms a six-helix claw that is similar to the catalytic core of the eukaryotic cyclic nucleotide phosphodiesterases. Most of the 29 sulfate ions bound to the Ppx dimer occupy sites where the polyP chain likely binds. An aqueduct that passes through the enzyme provides a physical basis for the enzyme's high processivity.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Ppx Dimer Interactions
(A) Stereoview of the homotypic association of αD helices, formed by a mixture of hydrophobic and hydrogen bond interactions.
(B) Stereoview of the heterotypic interactions formed between residues of domains II and IV.
Figure 4.
Figure 4. Sulfate Ions Bound to Ppx and the Polyphosphatase Active Site
(A) A surface representation of the Ppx dimer is shown with the 29 bound sulfate ions represented as CPK models. To monomer A, shown in darker shades of color, 12 sulfates are bound (S[A1]–S[A12]), whereas in monomer B, shown in lighter shades of color, 16 sulfates are bound (S[B1]–S[B16]). A single sulfate ion is bound at a site of symmetry between the two monomers (S[AB1]). The sulfate ions S[B5], S[A6], and S[B7] and S[A5], S[B6], and S[A7] are bound in the two aqueducts indicated by the arrows. See Figures S2C and S2D for a clearer view of the aqueducts.
(B) Superposition of domains II and IIA of E. coli Ppx and Thermotoga maritima FtsA (PDB code: 1E4G), respectively. The ATP nucleotide bound in FtsA is shown with the sulfate ions (S[A1]–S[A3]) bound in the active site of Ppx.
(C) The active site of monomer B is shown with the residues contacting the bound sulfate ions. Residues that contact the γ-phosphate of bound ATP in the other ASKHA members originate from loops that are structurally equivalent to those whose residues contact sulfate S[B1] in Ppx.
(D) The ATP nucleotide as bound in the active site of Thermotoga maritima FtsA (PDB code: 1E4G, ball-and-stick representation) is shown superimposed on the active site of Ppx monomer B (light green and red). If a nucleotide were present in the active site of Ppx, the side chains of residues N21, C169, and R267 (ball-and-stick representation) would clash with the ribose and adenine. These residues would therefore occlude ATP from the Ppx active site and allow binding only of a polyP chain.
 
  The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1263-1272) 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.  
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.  
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.