2job: Difference between revisions

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{{Seed}}
[[Image:2job.png|left|200px]]


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==Solution structure of an antilipopolysaccharide factor from shrimp and its possible Lipid A binding site==
The line below this paragraph, containing "STRUCTURE_2job", creates the "Structure Box" on the page.
<StructureSection load='2job' size='340' side='right'caption='[[2job]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2job]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Penaeus_monodon Penaeus monodon]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JOB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JOB FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 15 models</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=2job FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2job OCA], [https://pdbe.org/2job PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2job RCSB], [https://www.ebi.ac.uk/pdbsum/2job PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2job ProSAT]</span></td></tr>
{{STRUCTURE_2job|  PDB=2job  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/A5A3I5_PENMO A5A3I5_PENMO]
== 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/jo/2job_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2job ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The anti-lipopolysaccharide factor ALF-Pm3 is a 98-residue protein identified in hemocytes from the black tiger shrimp Penaeus monodon. It was expressed in Pichia pastoris from the constitutive glyceraldehyde-3-phosphate dehydrogenase promoter as a folded and (15)N uniformly labeled rALF-Pm3 protein. Its 3D structure was established by NMR and consists of three alpha-helices packed against a four-stranded beta-sheet. The C(34)--C(55) disulfide bond was shown to be essential for the structure stability. By using surface plasmon resonance, we demonstrated that rALF-Pm3 binds to LPS, lipid A and to OM(R)-174, a soluble analogue of lipid A. Biophysical studies of rALF-Pm3/LPS and rALF-Pm3/OM(R)-174 complexes indicated rather high molecular sized aggregates, which prevented us to experimentally determine by NMR the binding mode of these lipids to rALF-Pm3. However, on the basis of striking structural similarities to the FhuA/LPS complex, we designed an original model of the possible lipid A-binding site of ALF-Pm3. Such a binding site, located on the ALF-Pm3 beta-sheet and involving seven charged residues, is well conserved in ALF-L from Limulus polyphemus and in ALF-T from Tachypleus tridentatus. In addition, our model is in agreement with experiments showing that beta-hairpin synthetic peptides corresponding to ALF-L beta-sheet bind to LPS. Delineating lipid A-binding site of ALFs will help go further in the de novo design of new antibacterial or LPS-neutralizing drugs. (c) 2008 Wiley Periodicals, Inc. Biopolymers 91: 207-220, 2009.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com.


===Solution structure of an antilipopolysaccharide factor from shrimp and its possible Lipid A binding site===
NMR structure of rALF-Pm3, an anti-lipopolysaccharide factor from shrimp: Model of the possible lipid A-binding site.,Yang Y, Boze H, Chemardin P, Padilla A, Moulin G, Tassanakajon A, Pugniere M, Roquet F, Destoumieux-Garzon D, Gueguen Y, Bachere E, Aumelas A Biopolymers. 2009 Mar;91(3):207-20. PMID:19107926<ref>PMID:19107926</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_19107926}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2job" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 19107926 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_19107926}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2JOB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Penaeus_monodon Penaeus monodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JOB OCA].
 
==Reference==
NMR structure of rALF-Pm3, an anti-lipopolysaccharide factor from shrimp: Model of the possible lipid A-binding site., Yang Y, Boze H, Chemardin P, Padilla A, Moulin G, Tassanakajon A, Pugniere M, Roquet F, Destoumieux-Garzon D, Gueguen Y, Bachere E, Aumelas A, Biopolymers. 2009 Mar;91(3):207-20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19107926 19107926]
[[Category: Penaeus monodon]]
[[Category: Penaeus monodon]]
[[Category: Single protein]]
[[Category: Aumelas A]]
[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
[[Category: Bachere E]]
[[Category: Alf]]
[[Category: Boze H]]
[[Category: Endotoxin]]
[[Category: Chemardin P]]
[[Category: Lipid a binding protein]]
[[Category: Gueguen Y]]
[[Category: Lipid binding protein]]
[[Category: Moulin G]]
 
[[Category: Padilla A]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 28 20:25:54 2009''
[[Category: Pugniere M]]
[[Category: Roquet F]]
[[Category: Tassanakajon A]]
[[Category: Yang Y]]
Retrieved from "https://proteopedia.org/2job"