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1n7t

From Proteopedia

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ERBIN PDZ domain bound to a phage-derived peptide

Structural highlights

1n7t is a 2 chain structure with sequence from Homo sapiens. 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

ERBIN_HUMAN Acts as an adapter for the receptor ERBB2, in epithelia. By binding the unphosphorylated 'Tyr-1248' of receptor ERBB2, it may contribute to stabilize this unphosphorylated state (PubMed:16203728). Inhibits NOD2-dependent NF-kappa-B signaling and proinflammatory cytokine secretion (PubMed:16203728).^[1] ^[2]

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 LAP (leucine-rich repeat and PDZ-containing) family of proteins play a role in maintaining epithelial and neuronal cell size, and mutation of these proteins can have oncogenic consequences. The LAP protein Erbin has been implicated previously in a number of cellular activities by virtue of its PDZ domain-dependent association with the C termini of both ERB-B2 and the p120-catenins. The present work describes the NMR structure of Erbin PDZ in complex with a high affinity peptide ligand and includes a comprehensive energetic analysis of both the ligand and PDZ domain side chains responsible for binding. C-terminal phage display has been used to identify preferred ligands, whereas binding affinity measurements provide precise details of the energetic importance of each ligand side chain to binding. Alanine and homolog scanning mutagenesis (in a combinatorial phage display format) identifies Erbin side chains that make energetically important contacts with the ligand. The structure of a phage-optimized peptide (Ac-TGW(-4)ETW(-1)V; IC(50) = approximately 0.15 microm) in complex with Erbin PDZ provides a structural context to understand the binding energetics. In particular, the very favorable interactions with Trp(-1) are not Erbin side chain-mediated (and therefore may be generally applicable to many PDZ domains), whereas the beta2-beta3 loop provides a binding site for the Trp(-4) side chain (specific to Erbin because it has an unusually long loop). These results contribute to a growing appreciation for the importance of at least five ligand C-terminal side chains in determining PDZ domain binding energy and highlight the mechanisms of ligand discrimination among the several hundred PDZ domains present in the human genome.

Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain.,Skelton NJ, Koehler MF, Zobel K, Wong WL, Yeh S, Pisabarro MT, Yin JP, Lasky LA, Sidhu SS J Biol Chem. 2003 Feb 28;278(9):7645-54. Epub 2002 Nov 20. PMID:12446668^[3]

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

References

↑ Borg JP, Marchetto S, Le Bivic A, Ollendorff V, Jaulin-Bastard F, Saito H, Fournier E, Adelaide J, Margolis B, Birnbaum D. ERBIN: a basolateral PDZ protein that interacts with the mammalian ERBB2/HER2 receptor. Nat Cell Biol. 2000 Jul;2(7):407-14. PMID:10878805 doi:10.1038/35017038
↑ McDonald C, Chen FF, Ollendorff V, Ogura Y, Marchetto S, Lecine P, Borg JP, Nunez G. A role for Erbin in the regulation of Nod2-dependent NF-kappaB signaling. J Biol Chem. 2005 Dec 2;280(48):40301-9. doi: 10.1074/jbc.M508538200. Epub 2005, Oct 3. PMID:16203728 doi:http://dx.doi.org/10.1074/jbc.M508538200
↑ Skelton NJ, Koehler MF, Zobel K, Wong WL, Yeh S, Pisabarro MT, Yin JP, Lasky LA, Sidhu SS. Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain. J Biol Chem. 2003 Feb 28;278(9):7645-54. Epub 2002 Nov 20. PMID:12446668 doi:10.1074/jbc.M209751200

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/1n7t"

@@ Line 1: / Line 1: @@
 ==ERBIN PDZ domain bound to a phage-derived peptide==
-<StructureSection load='1n7t' size='340' side='right' caption='[[1n7t]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='1n7t' size='340' side='right'caption='[[1n7t]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1n7t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N7T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1n7t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N7T FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">erbin ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7t OCA], [http://pdbe.org/1n7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n7t RCSB], [http://www.ebi.ac.uk/pdbsum/1n7t PDBsum]</span></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=1n7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7t OCA], [https://pdbe.org/1n7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n7t RCSB], [https://www.ebi.ac.uk/pdbsum/1n7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n7t ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LAP2_HUMAN LAP2_HUMAN]] Acts as an adapter for the receptor ERBB2, in epithelia. By binding the unphosphorylated 'Tyr-1248' of receptor ERBB2, it may contribute to stabilize this unphosphorylated state.<ref>PMID:10878805</ref>
+[https://www.uniprot.org/uniprot/ERBIN_HUMAN ERBIN_HUMAN] Acts as an adapter for the receptor ERBB2, in epithelia. By binding the unphosphorylated 'Tyr-1248' of receptor ERBB2, it may contribute to stabilize this unphosphorylated state (PubMed:16203728). Inhibits NOD2-dependent NF-kappa-B signaling and proinflammatory cytokine secretion (PubMed:16203728).<ref>PMID:10878805</ref> <ref>PMID:16203728</ref>
 == 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/n7/1n7t_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/1n7t_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1n7t ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Koehler, M F.T]]
+[[Category: Large Structures]]
-[[Category: Lasky, L A]]
+[[Category: Koehler MFT]]
-[[Category: Pisabarro, M T]]
+[[Category: Lasky LA]]
-[[Category: Sidhu, S S]]
+[[Category: Pisabarro MT]]
-[[Category: Skelton, N J]]
+[[Category: Sidhu SS]]
-[[Category: Wong, W L]]
+[[Category: Skelton NJ]]
-[[Category: Yeh, S]]
+[[Category: Wong WL]]
-[[Category: Yin, J P]]
+[[Category: Yeh S]]
-[[Category: Zobel, K]]
+[[Category: Yin JP]]
-[[Category: C-terminal peptide complex]]
+[[Category: Zobel K]]
-[[Category: High affnity ligand]]
-[[Category: Pdz domain]]
-[[Category: Signaling protein]]

1n7t

From Proteopedia

Current revision

ERBIN PDZ domain bound to a phage-derived peptide

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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