1pot

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[[Image:1pot.gif|left|200px]]
 
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==SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (MONOMER FORM)==
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The line below this paragraph, containing "STRUCTURE_1pot", creates the "Structure Box" on the page.
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<StructureSection load='1pot' size='340' side='right'caption='[[1pot]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1pot]] is a 1 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=1POT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1POT FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.8&#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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{{STRUCTURE_1pot| PDB=1pot | SCENE= }}
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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=1pot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pot OCA], [https://pdbe.org/1pot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pot RCSB], [https://www.ebi.ac.uk/pdbsum/1pot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pot ProSAT]</span></td></tr>
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</table>
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'''SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (MONOMER FORM)'''
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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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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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The PotD protein from Escherichia coli is one of the components of the polyamine transport system present in the periplasm. This component specifically binds either spermidine or putrescine. The crystal structure of the E. coli PotD protein complexed with spermidine was solved at 1.8 A resolution and revealed the detailed substrate-binding mechanism. The structure provided the detailed conformation of the bound spermidine. Furthermore, a water molecule was clearly identified in the binding site lying between the amino-terminal domain and carboxyl-terminal domain. Through this water molecule, the bound spermidine molecule forms two hydrogen bonds with Thr 35 and Ser 211. Another periplasmic component of polyamine transport, the PotF protein, exhibits 35% sequence identity with the PotD protein, and it binds only putrescine, not spermidine. To understand these different substrate specificities, model building of the PotF protein was performed on the basis of the PotD crystal structure. The hypothetical structure suggests that the side chain of Lys 349 in PotF inhibits spermidine binding because of the repulsive forces between its positive charge and spermidine. On the other hand, putrescine could be accommodated into the binding site without any steric hindrance because its molecular size is much smaller than that of spermidine, and the positively charged amino group is relatively distant from Lys 349.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/po/1pot_consurf.spt"</scriptWhenChecked>
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1POT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1POT OCA].
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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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==Reference==
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</jmolCheckbox>
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The 1.8-A X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding., Sugiyama S, Matsuo Y, Maenaka K, Vassylyev DG, Matsushima M, Kashiwagi K, Igarashi K, Morikawa K, Protein Sci. 1996 Oct;5(10):1984-90. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8897598 8897598]
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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=1pot 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: Maenaka, K.]]
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[[Category: Maenaka K]]
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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: Binding protein]]
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[[Category: Polyamine transport protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 05:19:03 2008''
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Current revision

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

PDB ID 1pot

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