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PDBsum entry 2flo
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References listed in PDB file
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Key reference
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Title
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The structure of the exopolyphosphatase (ppx) from escherichia coli o157:h7 suggests a binding mode for long polyphosphate chains.
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Authors
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E.S.Rangarajan,
G.Nadeau,
Y.Li,
J.Wagner,
M.N.Hung,
J.D.Schrag,
M.Cygler,
A.Matte.
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Ref.
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J Mol Biol, 2006,
359,
1249-1260.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
359,
1249-1260)
copyright 2006.
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