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Structure

The structure is characterized by the actin-like ATPase domain that is a part of this superfamily. In Aquifex aeolicus it contains a ribonuclease H-like motif that is made up of a five-stranded ß-sheet with the second strand antiparallel to the rest. Strand 1 and 4 and strand 4 and 5 are connected by helical segments and are longer in the C-terminal domain than in the N-terminal domain. Five alpha-helices are located in the C-terminal domain and only two are located in the N-terminal domain. The type I structure represents a closed configuration. The more open arrangement of the domains displays rotational movement of the two domains around a single hinge region. The structural flexibility has been described as a "butterfly like" cleft opening around the active site.^[1]

Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member

In E. coli, exopolyphosphatase exists as a dimer, with each monomer consisting of four domains. The first two domains consist of three beta-sheets followed by an alpha-beta-alpha-beta-alpha fold. This is different from the previously described Aquifex aecolicus homolog which lacks the third and fourth domains.^[2]

Structure of an E. coli Exopolyphosphatase

Active Site

The active site of exopolyphosphatase is located in the clefts between domains I and II. This region contains a loop between strands beta-1 and beta-2 with Glu, two Ser, and an Asn residue that is critical for phosphate binding that is common among other ASKHA (acetate and sugar kinases, Hsp70, actin). The preference of exopolyphosphatase to bind to polyphosphate and not ATP has been contributed to the clashing that would occur between the ribose and adenosine of ATP and the side chains of N21, C169, and R267.^[2]

Mechanism

Arrow pushing mechanism for the activity of exopolyphosphatase

Exopolyphosphatase cleaves a terminal phosphate off of polyphosphate through the amino acid side chains of glutamate and lysine. Glutamate activates water, allowing it to act as a nucleophile and attack the terminal phosphate. Lysine acts as a general acid and donates a proton to the oxygen that was previously bridging the two phosphate atoms.

^ Kristensen, Ole; Laurberg, Martin; Liljas, Anders; Kastrup, Jette S.; Gajhede, Michael (2004). "Structural Characterization of the Stringent Response Related Exopolyphosphate/Guanosine Pentaphosphate Phosphohydrolase Protein Family". Biochemistry. 43: 8894–8900. doi:10.1021/bi049083c. PMID 15248747. {{cite journal}}: |access-date= requires |url= (help)
^ Alvarado, Johnjeff; Ghosh, Anita; Janovitz, Tyler; Jauregui, Andrew; Hasson, Miriam S.; Sanders, David A. (2006). "The Structure of the Exopolyphosphatase (PPX) from Escherichia coli O157:H7 Suggests a Binding Mode for Long Polyphosphate Chains". Journal of Molecular Biology. 359 (5): 1249–1260. doi:http://dx.doi.org/10.1016/j.jmb.2006.04.031. {{cite journal}}: |access-date= requires |url= (help); Check |doi= value (help); External link in |doi= (help)

[1] Kristensen, Ole; Laurberg, Martin; Liljas, Anders; Kastrup, Jette S.; Gajhede, Michael (2004). "Structural Characterization of the Stringent Response Related Exopolyphosphate/Guanosine Pentaphosphate Phosphohydrolase Protein Family". Biochemistry. 43: 8894–8900. doi:10.1021/bi049083c. PMID 15248747. {{cite journal}}: |access-date= requires |url= (help)

[2] Alvarado, Johnjeff; Ghosh, Anita; Janovitz, Tyler; Jauregui, Andrew; Hasson, Miriam S.; Sanders, David A. (2006). "The Structure of the Exopolyphosphatase (PPX) from Escherichia coli O157:H7 Suggests a Binding Mode for Long Polyphosphate Chains". Journal of Molecular Biology. 359 (5): 1249–1260. doi:http://dx.doi.org/10.1016/j.jmb.2006.04.031. {{cite journal}}: |access-date= requires |url= (help); Check |doi= value (help); External link in |doi= (help)

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