3if5: Difference between revisions

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 ==Crystal Structure Analysis of Mglu==
-<StructureSection load='3if5' size='340' side='right' caption='[[3if5]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
+<StructureSection load='3if5' size='340' side='right'caption='[[3if5]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3if5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacteridium_luteum"_schroeter_1872 "bacteridium luteum" schroeter 1872]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2dfw 2dfw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IF5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IF5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3if5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Micrococcus_luteus Micrococcus luteus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2dfw 2dfw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IF5 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Glutaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1270 "Bacteridium luteum" Schroeter 1872])</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]] 2.44&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutaminase Glutaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.2 3.5.1.2] </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=3if5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3if5 OCA], [https://pdbe.org/3if5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3if5 RCSB], [https://www.ebi.ac.uk/pdbsum/3if5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3if5 ProSAT]</span></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=3if5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3if5 OCA], [http://pdbe.org/3if5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3if5 RCSB], [http://www.ebi.ac.uk/pdbsum/3if5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3if5 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q4U1A6_MICLU Q4U1A6_MICLU]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=3if5 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Glutaminase from Micrococcus luteus K-3 [Micrococcus glutaminase (Mglu); 456 amino acid residues (aa); 48 kDa] is a salt-tolerant enzyme. Our previous study determined the structure of its major 42-kDa fragment. Here, using new crystallization conditions, we determined the structures of the intact enzyme in the presence and absence of its product L-glutamate and its activator Tris, which activates the enzyme by sixfold. With the exception of a 'lid' part (26-29 aa) and a few other short stretches, the structures were all very similar over the entire polypeptide chain. However, the presence of the ligands significantly reduced the length of the disordered regions: 41 aa in the unliganded structure (N), 21 aa for L-glutamate (G), 8 aa for Tris (T) and 6 aa for both L-glutamate and Tris (TG). L-glutamate was identified in both the G and TG structures, whereas Tris was only identified in the TG structure. Comparison of the glutamate-binding site between Mglu and salt-labile glutaminase (YbgJ) from Bacillus subtilis showed significantly smaller structural changes of the protein part in Mglu. A comparison of the substrate-binding pocket of Mglu, which is highly specific for L-glutamine, with that of Erwinia carotovora asparaginase, which has substrates other than L-glutamine, shows that Mglu has a larger substrate-binding pocket that prevents the binding of L-asparagine with proper interactions.
-Crystal structure of salt-tolerant glutaminase from Micrococcus luteus K-3 in the presence and absence of its product L-glutamate and its activator Tris.,Yoshimune K, Shirakihara Y, Wakayama M, Yumoto I FEBS J. 2010 Feb;277(3):738-48. Epub 2009 Dec 29. PMID:20050917<ref>PMID:20050917</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3if5" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Glutaminase|Glutaminase]]
+*[[Glutaminase 3D structures|Glutaminase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteridium luteum schroeter 1872]]
+[[Category: Large Structures]]
-[[Category: Glutaminase]]
+[[Category: Micrococcus luteus]]
-[[Category: Shirakihara, Y]]
+[[Category: Shirakihara Y]]
-[[Category: Yoshimune, K]]
+[[Category: Yoshimune K]]
-[[Category: Fragment]]
-[[Category: Hydrolase]]