2flo: Difference between revisions

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<StructureSection load='2flo' size='340' side='right'caption='[[2flo]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='2flo' size='340' side='right'caption='[[2flo]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2flo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Eco57 Eco57]. 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>
<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>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
</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>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ppx ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</td></tr>
<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>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exopolyphosphatase Exopolyphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.11 3.6.1.11] </span></td></tr>
<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>
<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>
</table>
</table>
== Function ==
== Function ==
[[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).  
[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).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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].
</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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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:16678853<ref>PMID:16678853</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2flo" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Eco57]]
[[Category: Escherichia coli O157:H7]]
[[Category: Exopolyphosphatase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Structural genomic]]
[[Category: Cygler M]]
[[Category: Cygler, M]]
[[Category: Matte A]]
[[Category: Matte, A]]
[[Category: Rangarajan ES]]
[[Category: Rangarajan, E S]]
[[Category: Bsgi]]
[[Category: Hydrolase]]
[[Category: Metaphosphatase]]
[[Category: Ppx/gppa]]
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