3drg: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:3drg.png|left|200px]]
-{{STRUCTURE_3drg|  PDB=3drg  |  SCENE=  }}
+==Lactococcal OppA complexed with bradykinin in the closed conformation==
+<StructureSection load='3drg' size='340' side='right'caption='[[3drg]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3drg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris_MG1363 Lactococcus lactis subsp. cremoris MG1363]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DRG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DRG 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]] 2.5&#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></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=3drg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3drg OCA], [https://pdbe.org/3drg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3drg RCSB], [https://www.ebi.ac.uk/pdbsum/3drg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3drg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A2RJ53_LACLM A2RJ53_LACLM]
+== 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/dr/3drg_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=3drg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Oligopeptide-binding protein A (OppA) from Lactococcus lactis binds peptides of an exceptionally wide range of lengths (4-35 residues), with no apparent sequence preference. Here, we present the crystal structures of OppA in the open- and closed-liganded conformations. The structures directly explain the protein's phenomenal promiscuity. A huge cavity allows binding of very long peptides, and a lack of constraints for the position of the N and C termini of the ligand is compatible with binding of peptides with varying lengths. Unexpectedly, the peptide's amino-acid composition (but not the exact sequence) appears to have a function in selection, with a preference for proline-rich peptides containing at least one isoleucine. These properties can be related to the physiology of the organism: L. lactis is auxotrophic for branched chain amino acids and favours proline-rich caseins as a source of amino acids. We propose a new mechanism for peptide selection based on amino-acid composition rather than sequence.
-===Lactococcal OppA complexed with bradykinin in the closed conformation===
+The structural basis for peptide selection by the transport receptor OppA.,Berntsson RP, Doeven MK, Fusetti F, Duurkens RH, Sengupta D, Marrink SJ, Thunnissen AM, Poolman B, Slotboom DJ EMBO J. 2009 Mar 19. PMID:19300437<ref>PMID:19300437</ref>
-{{ABSTRACT_PUBMED_19300437}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3drg" style="background-color:#fffaf0;"></div>
-[[3drg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DRG OCA].
 ==See Also==
+*[[ABC transporter 3D structures|ABC transporter 3D structures]]
 *[[Oligopeptide-binding protein|Oligopeptide-binding protein]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019300437</ref><references group="xtra"/>
+__TOC__
-[[Category: Lactococcus lactis]]
+</StructureSection>
-[[Category: Berntsson, R P.A.]]
+[[Category: Lactococcus lactis subsp. cremoris MG1363]]
-[[Category: Doeven, M K.]]
+[[Category: Large Structures]]
-[[Category: Duurkens, R H.]]
+[[Category: Berntsson RP-A]]
-[[Category: Marrink, S J.]]
+[[Category: Doeven MK]]
-[[Category: Poolman, B.]]
+[[Category: Duurkens RH]]
-[[Category: Sengupta, D.]]
+[[Category: Marrink S-J]]
-[[Category: Slotboom, D J.]]
+[[Category: Poolman B]]
-[[Category: Thunnissen, A M.]]
+[[Category: Sengupta D]]
-[[Category: Oligo-peptide binding]]
+[[Category: Slotboom D-J]]
-[[Category: Peptide binding protein]]
+[[Category: Thunnissen A-M]]
-[[Category: Venus fly-trap]]
-[[Category: Voluminous binding cavity]]