This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2job

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Solution structure of an antilipopolysaccharide factor from shrimp and its possible Lipid A binding site

Structural highlights

2job is a 1 chain structure with sequence from Penaeus monodon. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A5A3I5_PENMO

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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. NMR structure of rALF-Pm3, an anti-lipopolysaccharide factor from shrimp: Model of the possible lipid A-binding site. Biopolymers. 2009 Mar;91(3):207-20. PMID:19107926 doi:10.1002/bip.21119

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2job"

@@ Line 1: / Line 1: @@
 ==Solution structure of an antilipopolysaccharide factor from shrimp and its possible Lipid A binding site==
-<StructureSection load='2job' size='340' side='right'caption='[[2job]], [[NMR_Ensembles_of_Models | 15 NMR models]]' scene=''>
+<StructureSection load='2job' size='340' side='right'caption='[[2job]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2job]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Giant_tiger_prawn Giant tiger prawn]. 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 [http://proteopedia.org/fgij/fg.htm?mol=2JOB FirstGlance]. <br>
+<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>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2job FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2job OCA], [http://pdbe.org/2job PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2job RCSB], [http://www.ebi.ac.uk/pdbsum/2job PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2job ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A5A3I5_PENMO A5A3I5_PENMO]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 29: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Giant tiger prawn]]
 [[Category: Large Structures]]
-[[Category: Aumelas, A]]
+[[Category: Penaeus monodon]]
-[[Category: Bachere, E]]
+[[Category: Aumelas A]]
-[[Category: Boze, H]]
+[[Category: Bachere E]]
-[[Category: Chemardin, P]]
+[[Category: Boze H]]
-[[Category: Gueguen, Y]]
+[[Category: Chemardin P]]
-[[Category: Moulin, G]]
+[[Category: Gueguen Y]]
-[[Category: Padilla, A]]
+[[Category: Moulin G]]
-[[Category: Pugniere, M]]
+[[Category: Padilla A]]
-[[Category: Roquet, F]]
+[[Category: Pugniere M]]
-[[Category: Tassanakajon, A]]
+[[Category: Roquet F]]
-[[Category: Yang, Y]]
+[[Category: Tassanakajon A]]
-[[Category: Alf]]
+[[Category: Yang Y]]
-[[Category: Endotoxin]]
-[[Category: Lipid a binding protein]]
-[[Category: Lipid binding protein]]

2job

From Proteopedia

Current revision

Solution structure of an antilipopolysaccharide factor from shrimp and its possible Lipid A binding site

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox