Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 119.21 kDa 
• Atom Count: 8984 
• Modelled Residue Count: 998 
• Deposited Residue Count: 1026 
• Unique protein chains: 1

1U6Z

Structure of an E. coli Exopolyphosphatase: Insight into the processive hydrolysis of polyphosphate and its regulation

• DOI: 10.2210/pdb1U6Z/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-08-02 Released: 2005-12-06 
• Deposition Author(s): Hasson, M.S., Alvarado, J., Sanders, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.242 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 

Literature

Origin of exopolyphosphatase processivity: Fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog.

Alvarado, J., Ghosh, A., Janovitz, T., Jauregui, A., Hasson, M.S., Sanders, D.A.

(2006) Structure 14: 1263-1272

• PubMed: 16905100 
• DOI: 10.1016/j.str.2006.06.009
• Primary Citation of Related Structures:  
  1U6Z


• PubMed 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.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exopolyphosphatase	A, B	513	Escherichia coli	Mutation(s): 0  Gene Names: ppx EC: 3.6.1.11
Find proteins for P0AFL6 (Escherichia coli (strain K12)) Explore P0AFL6  Go to UniProtKB:  P0AFL6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth B],  BA [auth B],  C [auth A],  CA [auth B],  D [auth A],  DA [auth B],  E [auth A],  EA [auth B],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth B],  X [auth B],  Y [auth B],  Z [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.242 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.144	α = 90
b = 89.144	β = 90
c = 350.686	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-02 
• Released Date: 2005-12-06 
Deposition Author(s): Hasson, M.S., Alvarado, J., Sanders, D.A.

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance