1mki: Difference between revisions

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-[[Image:1mki.png|left|200px]]
-<!--
+==Crystal Structure of Bacillus Subtilis Probable Glutaminase, APC1040==
-The line below this paragraph, containing "STRUCTURE_1mki", creates the "Structure Box" on the page.
+<StructureSection load='1mki' size='340' side='right'caption='[[1mki]], [[Resolution|resolution]] 2.00&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'>[[1mki]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MKI 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]] 2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
-{{STRUCTURE_1mki|  PDB=1mki  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mki OCA], [https://pdbe.org/1mki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mki RCSB], [https://www.ebi.ac.uk/pdbsum/1mki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mki ProSAT], [https://www.topsan.org/Proteins/MCSG/1mki TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLSA1_BACSU GLSA1_BACSU]
+== 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/mk/1mki_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=1mki ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Glutaminases belong to the large superfamily of serine-dependent beta-lactamases and penicillin-binding proteins, and they catalyze the hydrolytic deamidation of L-glutamine to L-glutamate. In this work, we purified and biochemically characterized four predicted glutaminases from Escherichia coli (YbaS and YneH) and Bacillus subtilis (YlaM and YbgJ). The proteins demonstrated strict specificity to L-glutamine and did not hydrolyze D-glutamine or L-asparagine. In each organism, one glutaminase showed higher affinity to glutamine ( E. coli YbaS and B. subtilis YlaM; K m 7.3 and 7.6 mM, respectively) than the second glutaminase ( E. coli YneH and B. subtilis YbgJ; K m 27.6 and 30.6 mM, respectively). The crystal structures of the E. coli YbaS and the B. subtilis YbgJ revealed the presence of a classical beta-lactamase-like fold and conservation of several key catalytic residues of beta-lactamases (Ser74, Lys77, Asn126, Lys268, and Ser269 in YbgJ). Alanine replacement mutagenesis demonstrated that most of the conserved residues located in the putative glutaminase catalytic site are essential for activity. The crystal structure of the YbgJ complex with the glutaminase inhibitor 6-diazo-5-oxo- l-norleucine revealed the presence of a covalent bond between the inhibitor and the hydroxyl oxygen of Ser74, providing evidence that Ser74 is the primary catalytic nucleophile and that the glutaminase reaction proceeds through formation of an enzyme-glutamyl intermediate. Growth experiments with the E. coli glutaminase deletion strains revealed that YneH is involved in the assimilation of l-glutamine as a sole source of carbon and nitrogen and suggested that both glutaminases (YbaS and YneH) also contribute to acid resistance in E. coli.
-===Crystal Structure of Bacillus Subtilis Probable Glutaminase, APC1040===
+Functional and structural characterization of four glutaminases from Escherichia coli and Bacillus subtilis.,Brown G, Singer A, Proudfoot M, Skarina T, Kim Y, Chang C, Dementieva I, Kuznetsova E, Gonzalez CF, Joachimiak A, Savchenko A, Yakunin AF Biochemistry. 2008 May 27;47(21):5724-35. Epub 2008 May 6. PMID:18459799<ref>PMID:18459799</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1mki" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18459799}}, adds the Publication Abstract to the page
+*[[Glutaminase 3D structures|Glutaminase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18459799 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18459799}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[1mki]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MKI OCA].
-==Reference==
-<ref group="xtra">PMID:018459799</ref><references group="xtra"/>
 [[Category: Bacillus subtilis]]
-[[Category: Glutaminase]]
+[[Category: Large Structures]]
-[[Category: Dementieva, I.]]
+[[Category: Dementieva I]]
-[[Category: Joachimiak, A.]]
+[[Category: Joachimiak A]]
-[[Category: Kim, Y.]]
+[[Category: Kim Y]]
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+[[Category: Vinokour E]]
-[[Category: Vinokour, E.]]
-[[Category: Hydrolase]]
-[[Category: Mcsg]]
-[[Category: Midwest center for structural genomic]]
-[[Category: Probable glutaminase]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Structural genomic]]