1tf9: Difference between revisions

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 ==Streptomyces griseus aminopeptidase complexed with P-Iodo-L-Phenylalanine==
-<StructureSection load='1tf9' size='340' side='right' caption='[[1tf9]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
+<StructureSection load='1tf9' size='340' side='right'caption='[[1tf9]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1tf9]] is a 1 chain structure 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=1TF9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TF9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1tf9]] 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=1TF9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TF9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xjo|1xjo]], [[1cp7|1cp7]], [[1qq9|1qq9]], [[1f2p|1f2p]], [[1f2o|1f2o]], [[1tf8|1tf8]]</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=PHI:IODO-PHENYLALANINE'>PHI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1tf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tf9 OCA], [http://pdbe.org/1tf9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tf9 RCSB], [http://www.ebi.ac.uk/pdbsum/1tf9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tf9 ProSAT]</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=1tf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tf9 OCA], [https://pdbe.org/1tf9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tf9 RCSB], [https://www.ebi.ac.uk/pdbsum/1tf9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tf9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/APX_STRGR APX_STRGR]] Specific for larger hydrophobic acids, especially leucine. No cleavage occurs if the next residue is proline.
+[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]]
@@ Line 20: / Line 20: @@
 </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=1tf9 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.
-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>
-<div class="pdbe-citations 1tf9" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Aminopeptidase|Aminopeptidase]]
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
 *[[Streptomyces griseus Aminopeptidase (SGAP)|Streptomyces griseus Aminopeptidase (SGAP)]]
 == References ==
@@ Line 37: / Line 28: @@
 __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]]