1tf8: Difference between revisions

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-[[Image:1tf8.png|left|200px]]
-<!--
+==Streptomyces griseus aminopeptidase complexed with L-tryptophan==
-The line below this paragraph, containing "STRUCTURE_1tf8", creates the "Structure Box" on the page.
+<StructureSection load='1tf8' size='340' side='right'caption='[[1tf8]], [[Resolution|resolution]] 1.30&Aring;' 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'>[[1tf8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TF8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TF8 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">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1tf8|  PDB=1tf8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tf8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tf8 OCA], [https://pdbe.org/1tf8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tf8 RCSB], [https://www.ebi.ac.uk/pdbsum/1tf8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tf8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/APX_STRGG APX_STRGG] An exopeptidase specific for larger hydrophobic amino acids (especially leucine), no cleavage occurs if the next residue is proline (PubMed:8444149).<ref>PMID:2503378</ref> <ref>PMID:8444149</ref> <ref>PMID:8665903</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/tf/1tf8_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=1tf8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The bacterial aminopeptidase isolated from the extracellular extract of Streptomyces griseus (SGAP) is a double-zinc exopeptidase with a high preference for large hydrophobic amino-terminus residues. It is a monomer of a relatively low molecular weight (30 kDa), is heat-stable, displays a high and efficient catalytic turnover and its activity is modulated by calcium ions. Several free amino acids were found to inhibit the activity of SGAP in the millimolar concentration range and can therefore serve for the study of binding of both inhibitors and reaction products. The current study is focused on the X-ray crystallographic analysis of the SGAP complexes with L-tryptophan and p-iodo-L-phenylalanine, both at 1.30 A resolution. These two bulky inhibitory amino acids were found to bind to the active site of SGAP in very similar positions and orientations. Both of them bind to the two active-site zinc ions via their free carboxylate group, while displacing the zinc-bound water/hydroxide that is present in the native enzyme. Further stabilization of the binding of the amino-acid carboxylate group is achieved by its relatively strong interactions with the hydroxyl group of Tyr246 and the carboxylate group of Glu131. The binding is also stabilized by three specific hydrogen bonds between the amine group of the bound amino acid and enzyme residues Glu131, Asp160 and Arg202. These consistent interactions confirm the key role of these residues in the specific binding of the free amine of substrates and products, as proposed previously. The phenyl ring of Phe219 of the enzyme is involved in stacking interactions with the corresponding aromatic ring of the bound affector. This interaction seems to be important for the binding and orientation of the aromatic side chain within the specificity pocket. These structural results correlate well with the results obtained for the complexes of SGAP with other inhibitory amino acids and support the general catalytic mechanism proposed for this and related enzymes.
-===Streptomyces griseus aminopeptidase complexed with L-tryptophan===
+Binding of inhibitory aromatic amino acids to Streptomyces griseus aminopeptidase.,Reiland V, Gilboa R, Spungin-Bialik A, Schomburg D, Shoham Y, Blumberg S, Shoham G Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1738-46. Epub 2004, Sep 23. PMID:15388919<ref>PMID:15388919</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15388919}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1tf8" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15388919 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_15388919}}
-==About this Structure==
-[[1tf8]] is a 1 chain structure of [[Streptomyces griseus Aminopeptidase (SGAP)]] with sequence from [http://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TF8 OCA].
 ==See Also==
-*[[Streptomyces griseus Aminopeptidase (SGAP)]]
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
+*[[Streptomyces griseus Aminopeptidase (SGAP)|Streptomyces griseus Aminopeptidase (SGAP)]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:15388919</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptomyces griseus]]
-[[Category: Blumberg, S.]]
+[[Category: Blumberg S]]
-[[Category: Gilboa, R.]]
+[[Category: Gilboa R]]
-[[Category: Reiland, V.]]
+[[Category: Reiland V]]
-[[Category: Schomburg, D.]]
+[[Category: Schomburg D]]
-[[Category: Shoham, G.]]
+[[Category: Shoham G]]
-[[Category: Shoham, Y.]]
+[[Category: Shoham Y]]
-[[Category: Spungin-Bialik, A.]]
+[[Category: Spungin-Bialik A]]
-[[Category: Calcium activation]]
-[[Category: Double-zinc metalloproteinase]]
-[[Category: Hydrolase]]
-[[Category: Protein-inhibitor complex]]