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2flo

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(New page: 200px<br /><applet load="2flo" size="450" color="white" frame="true" align="right" spinBox="true" caption="2flo, resolution 2.20&Aring;" /> '''Crystal structure of...)
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[[Image:2flo.gif|left|200px]]<br /><applet load="2flo" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2flo, resolution 2.20&Aring;" />
 
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'''Crystal structure of exopolyphosphatase (PPX) from E. coli O157:H7'''<br />
 
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==Overview==
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==Crystal structure of exopolyphosphatase (PPX) from E. coli O157:H7==
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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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<StructureSection load='2flo' size='340' side='right'caption='[[2flo]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2flo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FLO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FLO FirstGlance]. <br>
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2FLO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Exopolyphosphatase Exopolyphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.11 3.6.1.11] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FLO OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2flo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2flo OCA], [https://pdbe.org/2flo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2flo RCSB], [https://www.ebi.ac.uk/pdbsum/2flo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2flo ProSAT], [https://www.topsan.org/Proteins/BSGI/2flo TOPSAN]</span></td></tr>
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The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains., Rangarajan ES, Nadeau G, Li Y, Wagner J, Hung MN, Schrag JD, Cygler M, Matte A, J Mol Biol. 2006 Jun 23;359(5):1249-60. Epub 2006 Apr 27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16678853 16678853]
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</table>
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[[Category: Escherichia coli]]
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== Function ==
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[[Category: Exopolyphosphatase]]
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[https://www.uniprot.org/uniprot/PPX_ECO57 PPX_ECO57] Degradation of inorganic polyphosphates. Orthophosphate is released progressively from the ends of polyphosphate of circa 500 residues long, while chains of circa 15 residues compete poorly with polyphosphate as substrate (By similarity).
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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: BSGI, Montreal-Kingston.Bacterial.Structural.Genomics.Initiative.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Cygler, M.]]
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Check<jmol>
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[[Category: Matte, A.]]
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<jmolCheckbox>
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[[Category: Rangarajan, E.S.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fl/2flo_consurf.spt"</scriptWhenChecked>
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[[Category: bacterial structural genomics]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: bsgi]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: exopolyphosphatase]]
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</jmolCheckbox>
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[[Category: metaphosphatase]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2flo ConSurf].
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[[Category: montreal-kingston bacterial structural genomics initiative]]
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<div style="clear:both"></div>
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[[Category: ppx/gppa]]
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__TOC__
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[[Category: structural genomics]]
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</StructureSection>
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[[Category: Escherichia coli O157:H7]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:37:18 2007''
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[[Category: Large Structures]]
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[[Category: Cygler M]]
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[[Category: Matte A]]
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[[Category: Rangarajan ES]]

Current revision

Crystal structure of exopolyphosphatase (PPX) from E. coli O157:H7

PDB ID 2flo

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