2e1m: Difference between revisions

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-{{Seed}}
-[[Image:2e1m.png|left|200px]]
-<!--
+==Crystal Structure of L-Glutamate Oxidase from Streptomyces sp. X-119-6==
-The line below this paragraph, containing "STRUCTURE_2e1m", creates the "Structure Box" on the page.
+<StructureSection load='2e1m' size='340' side='right'caption='[[2e1m]], [[Resolution|resolution]] 2.80&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'>[[2e1m]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._X-119-6 Streptomyces sp. X-119-6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1M 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]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_2e1m|  PDB=2e1m  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1m OCA], [https://pdbe.org/2e1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e1m RCSB], [https://www.ebi.ac.uk/pdbsum/2e1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8L3C7_9ACTN Q8L3C7_9ACTN]
+== 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/e1/2e1m_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=2e1m ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+L-Glutamate oxidase (LGOX) from Streptomyces sp. X-119-6, which catalyzes the oxidative deamination of L-glutamate, has attracted increasing attention as a component of amperometric L-glutamate sensors used in the food industry and clinical biochemistry. The precursor of LGOX, which has a homodimeric structure, is less active than the mature enzyme with an alpha(2)beta(2)V(2) structure; enzymatic proteolysis of the precursor forms the stable mature enzyme. We solved the crystal structure of mature LGOX using molecular replacement with a structurally homologous model of L-amino acid oxidase (LAAO) from snake venom: LGOX has a deeply buried active site and two entrances from the surface of the protein into the active site. Comparison of the LGOX structure with that of LAAO revealed that LGOX has three regions that are absent from the LAAO structure, one of which is involved in the formation of the entrance. Furthermore, the arrangement of the residues composing the active site differs between LGOX and LAAO, and the active site of LGOX is narrower than that of LAAO. Results of the comparative analyses described herein raise the possibility that such a unique structure of LGOX is associated with its substrate specificity.
-===Crystal Structure of L-Glutamate Oxidase from Streptomyces sp. X-119-6===
+Structural characterization of L-glutamate oxidase from Streptomyces sp. X-119-6.,Arima J, Sasaki C, Sakaguchi C, Mizuno H, Tamura T, Kashima A, Kusakabe H, Sugio S, Inagaki K FEBS J. 2009 Jul;276(14):3894-903. Epub 2009 Jun 15. PMID:19531050<ref>PMID:19531050</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_19531050}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2e1m" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19531050 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19531050}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-E1M is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1M OCA].
+[[Category: Streptomyces sp. X-119-6]]
+[[Category: Arima J]]
-==Reference==
+[[Category: Inagaki K]]
-<ref group="xtra">PMID:19531050</ref><references group="xtra"/>
+[[Category: Kashima A]]
-[[Category: Bacteria]]
+[[Category: Kusakabe H]]
-[[Category: L-glutamate oxidase]]
+[[Category: Mizuno H]]
-[[Category: Arima, J.]]
+[[Category: Sakaguchi C]]
-[[Category: Inagaki, K.]]
+[[Category: Sasaki C]]
-[[Category: Kashima, A.]]
+[[Category: Sugio S]]
-[[Category: Kusakabe, H.]]
+[[Category: Tamura T]]
-[[Category: Mizuno, H.]]
-[[Category: Sakaguchi, C.]]
-[[Category: Sasaki, C.]]
-[[Category: Sugio, S.]]
-[[Category: Tamura, T.]]
-[[Category: 3d-structure]]
-[[Category: Fad]]
-[[Category: Flavoprotein]]
-[[Category: L-amino acid oxidase]]
-[[Category: L-glutamate oxidase]]
-[[Category: L-gox]]
-[[Category: Oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat Jul  4 18:01:26 2009''