1xdp

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[[Image:1xdp.gif|left|200px]]<br /><applet load="1xdp" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1xdp, resolution 2.50&Aring;" />
 
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'''Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP'''<br />
 
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==Overview==
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==Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP==
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Polyphosphate (polyP), a linear polymer of hundreds of orthophosphate residues, exists in all tested cells in nature, from pathogenic bacteria to mammals. In bacteria, polyP has a crucial role in stress responses and stationary-phase survival. Polyphosphate kinase (PPK) is the principal enzyme that catalyses the synthesis of polyP in bacteria. It has been shown that PPK is required for bacterial motility, biofilm formation and the production of virulence factors. PPK inhibitors may thus provide a unique therapeutic opportunity against antibiotic-resistant pathogens. Here, we report crystal structures of full-length Escherichia coli PPK and its complex with AMPPNP (beta-gamma-imidoadenosine 5-phosphate). PPK forms an interlocked dimer, with each 80 kDa monomer containing four structural domains. The PPK active site is located in a tunnel, which contains a unique ATP-binding pocket and may accommodate the translocation of synthesized polyP. The PPK structure has laid the foundation for understanding the initiation of polyP synthesis by PPK.
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<StructureSection load='1xdp' size='340' side='right'caption='[[1xdp]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1xdp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XDP FirstGlance]. <br>
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1XDP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=ATP:'>ATP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Polyphosphate_kinase Polyphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.1 2.7.4.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XDP 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]] 2.5&#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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1xdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdp OCA], [https://pdbe.org/1xdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xdp RCSB], [https://www.ebi.ac.uk/pdbsum/1xdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdp ProSAT]</span></td></tr>
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Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis., Zhu Y, Huang W, Lee SS, Xu W, EMBO Rep. 2005 Jul;6(7):681-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15947782 15947782]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PPK1_ECOLI PPK1_ECOLI] Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP). Can form linear polymers of orthophosphate with chain lengths up to 1000 or more. Can use GTP instead of ATP, but the efficiency of GTP is 5% that of ATP. Also exhibits several other enzymatic activities, which include: ATP synthesis from polyP in the presence of excess ADP, general nucleoside-diphosphate kinase activity, linear guanosine 5'-tetraphosphate (ppppG) synthesis and autophosphorylation.<ref>PMID:10660553</ref> <ref>PMID:8962061</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdp_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1xdp ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Polyphosphate kinase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Huang W]]
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[[Category: Huang, W.]]
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[[Category: Lee SS]]
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[[Category: Lee, S S.]]
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[[Category: Xu W]]
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[[Category: Xu, W.]]
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[[Category: Zhu Y]]
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[[Category: Zhu, Y.]]
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[[Category: ATP]]
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[[Category: MG]]
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[[Category: amppnp]]
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[[Category: e coli polyphosphate kinase]]
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[[Category: ppk]]
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[[Category: ppk complex with amppnp]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:53:42 2008''
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Current revision

Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP

PDB ID 1xdp

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