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1poy

From Proteopedia

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(New page: 200px<br /><applet load="1poy" size="450" color="white" frame="true" align="right" spinBox="true" caption="1poy, resolution 2.5&Aring;" /> '''SPERMIDINE/PUTRESCINE...)
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[[Image:1poy.jpg|left|200px]]<br /><applet load="1poy" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1poy, resolution 2.5&Aring;" />
 
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'''SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM)'''<br />
 
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==Overview==
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==SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM)==
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PotD protein is a periplasmic binding protein and the primary receptor of, the polyamine transport system, which regulates the polyamine content in, Escherichia coli. The crystal structure of PotD in complex with spermidine, has been solved at 2.5-A resolution. The PotD protein consists of two, domains with an alternating beta-alpha-beta topology. The polyamine, binding site is in a central cleft lying in the interface between the, domains. In the cleft, four acidic residues recognize the three positively, charged nitrogen atoms of spermidine, while five aromatic side chains, anchor the methylene backbone by van der Waals interactions. The overall, fold of PotD is similar to that of other periplasmic binding proteins, and, in particular to the maltodextrin-binding protein from E. coli, despite, the fact that sequence identity is as low as 20%. The comparison of the, PotD structure with the two maltodextrin-binding protein structures, determined in the presence and absence of the substrate, suggests that, spermidine binding rearranges the relative orientation of the PotD domains, to create a more compact structure.
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<StructureSection load='1poy' size='340' side='right'caption='[[1poy]], [[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'>[[1poy]] is a 4 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=1POY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1POY FirstGlance]. <br>
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1POY 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 SPD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1POY 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=SPD:SPERMIDINE'>SPD</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=1poy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1poy OCA], [https://pdbe.org/1poy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1poy RCSB], [https://www.ebi.ac.uk/pdbsum/1poy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1poy ProSAT]</span></td></tr>
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Crystal structure of PotD, the primary receptor of the polyamine transport system in Escherichia coli., Sugiyama S, Vassylyev DG, Matsushima M, Kashiwagi K, Igarashi K, Morikawa K, J Biol Chem. 1996 Apr 19;271(16):9519-25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8621624 8621624]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/POTD_ECOLI POTD_ECOLI] Required for the activity of the bacterial periplasmic transport system of putrescine and spermidine. Polyamine binding protein.
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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/po/1poy_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=1poy ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Matsushima, M.]]
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[[Category: Matsushima M]]
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[[Category: Morikawa, K.]]
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[[Category: Morikawa K]]
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[[Category: Sugiyama, S.]]
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[[Category: Sugiyama S]]
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[[Category: Vassylyev, D.G.]]
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[[Category: Vassylyev DG]]
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[[Category: SPD]]
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[[Category: binding protein]]
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[[Category: transport protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:59:08 2007''
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Current revision

SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM)

PDB ID 1poy

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