1edy: Difference between revisions

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

OCA

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-[[Image:1edy.gif|left|200px]]<br /><applet load="1edy" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1edy, resolution 2.3&Aring;" />
-'''CRYSTAL STRUCTURE OF RAT ALPHA 1-MACROGLOBULIN RECEPTOR BINDING DOMAIN'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF RAT ALPHA 1-MACROGLOBULIN RECEPTOR BINDING DOMAIN==
-Alpha-macroglobulin inhibits a broad spectrum of proteinases by forming, macromolecular cages inside which proteinases are cross-linked and, trapped. Upon formation of a complex with proteinase, alpha-macroglobulin, undergoes a large conformational change that results in the exposure of, its receptor-binding domain (RBD). Engagement of this domain by, alpha-macroglobulin receptor permits clearance of the alpha-macroglobulin:, proteinase complex from circulation. The crystal structure of rat, alpha1-macroglobulin RBD has been determined at 2.3 A resolution. The RBD, is composed of a nine-stranded beta-sandwich and a single alpha-helix that, has been implicated as part of the receptor binding site and that lies on, the surface of the beta-sandwich. The crystallographic asymmetric unit, contains a dimer of RBDs related by approximate twofold symmetry such that, the putative receptor recognition sites of the two monomers are, contiguous. By gel filtration and ultracentrifugation, it is shown that, RBD dimers form in solution with a dissociation constant of approximately, 50 microM. The structure of the RBD dimer might mimic a conformation of, transformed alpha-macroglobulin in which the proposed receptor binding, residues are exposed on one face of the dimer. A pair of phenylalanine, residues replaces a cystine that is conserved in other members of the, macroglobulin family. These residues participate in a network of aromatic, side-chain interactions that appears to stabilize the dimer interface.
+<StructureSection load='1edy' size='340' side='right'caption='[[1edy]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1edy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EDY FirstGlance]. <br>
-EDY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EDY OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</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=1edy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1edy OCA], [https://pdbe.org/1edy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1edy RCSB], [https://www.ebi.ac.uk/pdbsum/1edy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1edy ProSAT]</span></td></tr>
-==Reference==
+</table>
-Structure of a rat alpha 1-macroglobulin receptor-binding domain dimer., Xiao T, DeCamp DL, Spran SR, Protein Sci. 2000 Oct;9(10):1889-97. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11106161 11106161]
+== Function ==
+[https://www.uniprot.org/uniprot/A1M_RAT A1M_RAT] Is able to inhibit all four classes of proteinases by a unique 'trapping' mechanism. This protein has a peptide stretch, called the 'bait region' which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein which traps the proteinase. The entrapped enzyme remains active against low molecular weight substrates (activity against high molecular weight substrates is greatly reduced). Following cleavage in the bait region a thioester bond is hydrolyzed and mediates the covalent binding of the protein to the proteinase (By similarity).[UniProtKB:P01023]
+== 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/ed/1edy_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=1edy ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: DeCamp DL]]
-[[Category: DeCamp, D.L.]]
+[[Category: Sprang SR]]
-[[Category: Sprang, S.R.]]
+[[Category: Xiao T]]
-[[Category: Xiao, T.]]
-[[Category: beta sandwich]]
-[[Category: pseudo-symmetric dimer]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:55:52 2007''