2v84: Difference between revisions

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[[Image:2v84.jpg|left|200px]]
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{{STRUCTURE_2v84|  PDB=2v84  |  SCENE=  }}
'''CRYSTAL STRUCTURE OF THE TP0655 (TPPOTD) LIPOPROTEIN OF TREPONEMA PALLIDUM'''


==Crystal Structure of the Tp0655 (TpPotD) Lipoprotein of Treponema pallidum==
<StructureSection load='2v84' size='340' side='right'caption='[[2v84]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2v84]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Treponema_pallidum_subsp._pallidum_str._Nichols Treponema pallidum subsp. pallidum str. Nichols]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V84 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.78&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></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=2v84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v84 OCA], [https://pdbe.org/2v84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v84 RCSB], [https://www.ebi.ac.uk/pdbsum/2v84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v84 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O83661_TREPA O83661_TREPA]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v8/2v84_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2v84 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Tp0655 of Treponema pallidum, the causative agent of syphilis, is predicted to be a 40 kDa membrane lipoprotein. Previous sequence analysis of Tp0655 noted its homology to polyamine-binding proteins of the bacterial PotD family, which serve as periplasmic ligand-binding proteins of ATP-binding-cassette (ABC) transport systems. Here, the 1.8 A crystal structure of Tp0655 demonstrated structural homology to Escherichia coli PotD and PotF. The latter two proteins preferentially bind spermidine and putrescine, respectively. All of these proteins contain two domains that sandwich the ligand between them. The ligand-binding site of Tp0655 can be occupied by 2-(N-morpholino)ethanesulfanoic acid, a component of the crystallization medium. To discern the polyamine binding preferences of Tp0655, the protein was subjected to isothermal titration calorimetric experiments. The titrations established that Tp0655 binds polyamines avidly, with a marked preference for putrescine (Kd=10 nM) over spermidine (Kd=430 nM), but the related compounds cadaverine and spermine did not bind. Structural comparisons and structure-based sequence analyses provide insights into how polyamine-binding proteins recognize their ligands. In particular, these comparisons allow the derivation of rules that may be used to predict the function of other members of the PotD family. The sequential, structural, and functional homology of Tp0655 to PotD and PotF prompt the conclusion that the former likely is the polyamine-binding component of an ABC-type polyamine transport system in T. pallidum. We thus rename Tp0655 as TpPotD. The ramifications of TpPotD as a polyamine-binding protein to the parasitic strategy of T. pallidum are discussed.


==Overview==
Structural and biochemical basis for polyamine binding to the Tp0655 lipoprotein of Treponema pallidum: putative role for Tp0655 (TpPotD) as a polyamine receptor.,Machius M, Brautigam CA, Tomchick DR, Ward P, Otwinowski Z, Blevins JS, Deka RK, Norgard MV J Mol Biol. 2007 Oct 26;373(3):681-94. Epub 2007 Aug 21. PMID:17868688<ref>PMID:17868688</ref>
Tp0655 of Treponema pallidum, the causative agent of syphilis, is predicted to be a 40 kDa membrane lipoprotein. Previous sequence analysis of Tp0655 noted its homology to polyamine-binding proteins of the bacterial PotD family, which serve as periplasmic ligand-binding proteins of ATP-binding-cassette (ABC) transport systems. Here, the 1.8 A crystal structure of Tp0655 demonstrated structural homology to Escherichia coli PotD and PotF. The latter two proteins preferentially bind spermidine and putrescine, respectively. All of these proteins contain two domains that sandwich the ligand between them. The ligand-binding site of Tp0655 can be occupied by 2-(N-morpholino)ethanesulfanoic acid, a component of the crystallization medium. To discern the polyamine binding preferences of Tp0655, the protein was subjected to isothermal titration calorimetric experiments. The titrations established that Tp0655 binds polyamines avidly, with a marked preference for putrescine (Kd=10 nM) over spermidine (Kd=430 nM), but the related compounds cadaverine and spermine did not bind. Structural comparisons and structure-based sequence analyses provide insights into how polyamine-binding proteins recognize their ligands. In particular, these comparisons allow the derivation of rules that may be used to predict the function of other members of the PotD family. The sequential, structural, and functional homology of Tp0655 to PotD and PotF prompt the conclusion that the former likely is the polyamine-binding component of an ABC-type polyamine transport system in T. pallidum. We thus rename Tp0655 as TpPotD. The ramifications of TpPotD as a polyamine-binding protein to the parasitic strategy of T. pallidum are discussed.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2V84 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Treponema_pallidum Treponema pallidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V84 OCA].
</div>
<div class="pdbe-citations 2v84" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structural and biochemical basis for polyamine binding to the Tp0655 lipoprotein of Treponema pallidum: putative role for Tp0655 (TpPotD) as a polyamine receptor., Machius M, Brautigam CA, Tomchick DR, Ward P, Otwinowski Z, Blevins JS, Deka RK, Norgard MV, J Mol Biol. 2007 Oct 26;373(3):681-94. Epub 2007 Aug 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17868688 17868688]
*[[ABC transporter 3D structures|ABC transporter 3D structures]]
[[Category: Single protein]]
== References ==
[[Category: Treponema pallidum]]
<references/>
[[Category: Blevine, J S.]]
__TOC__
[[Category: Brautigam, C A.]]
</StructureSection>
[[Category: Deka, R K.]]
[[Category: Large Structures]]
[[Category: Machius, M.]]
[[Category: Treponema pallidum subsp. pallidum str. Nichols]]
[[Category: Norgard, M V.]]
[[Category: Blevine JS]]
[[Category: Otwinowski, Z.]]
[[Category: Brautigam CA]]
[[Category: Tomchick, D R.]]
[[Category: Deka RK]]
[[Category: Ward, P.]]
[[Category: Machius M]]
[[Category: Abc transporter]]
[[Category: Norgard MV]]
[[Category: Lipoprotein]]
[[Category: Otwinowski Z]]
[[Category: Polyamine binding]]
[[Category: Tomchick DR]]
[[Category: Putrescine]]
[[Category: Ward P]]
[[Category: Spermidine]]
[[Category: Syphili]]
[[Category: Transport protein]]
[[Category: Treponema pallidum]]
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