1e2o: Difference between revisions

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-{{Seed}}
-[[Image:1e2o.png|left|200px]]
-<!--
+==CATALYTIC DOMAIN FROM DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE==
-The line below this paragraph, containing "STRUCTURE_1e2o", creates the "Structure Box" on the page.
+<StructureSection load='1e2o' size='340' side='right'caption='[[1e2o]], [[Resolution|resolution]] 3.00&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'>[[1e2o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The October 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Citric Acid Cycle''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_10 10.2210/rcsb_pdb/mom_2012_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E2O 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]] 3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1e2o|  PDB=1e2o  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1e2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e2o OCA], [https://pdbe.org/1e2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e2o RCSB], [https://www.ebi.ac.uk/pdbsum/1e2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e2o ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ODO2_ECOLI ODO2_ECOLI] The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3).
+== 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/e2/1e2o_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=1e2o ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The dihydrolipoamide succinyltransferase (E2o) component of the 2-oxoglutarate dehydrogenase multienzyme complex is composed of 24 subunits arranged with 432 point group symmetry. The catalytic domain (CD) of the E2o component catalyzes the transfer of a succinyl group from the S-succinyldihydrolipoyl moiety to coenzyme A. The crystal structure of the Escherichia coli E2oCD has been solved to 3.0 A resolution using molecular replacement phases derived from the structure of the catalytic domain from the Azotobacter vinelandii dihydrolipoamide acetyltransferase (E2pCD). The refined model of the E. coli E2oCD consists of residues 172 to 404 and has an R-factor of 0.205 (Rfree=0.249) for 9696 reflections between 20.0 and 3.0 A resolution. Although both E2oCD and E2pCD form 24mers, subtle changes in the orientations of two helices in E2oCD increase the stability of the E2oCD 24mer in comparison to the less stable A. vinelandii E2pCD 24mer. Like E2pCD and chloramphenicol acetyltransferase (CAT), the active site of E2oCD is located in the middle of a channel formed at the interface between two 3-fold related subunits. Two of the active-site residues (His375 and Thr323) have a similar orientation to their counterparts in E2pCD and CAT. A third catalytic residue (Asp379) assumes a conformation similar to the corresponding residue in E2pCD (Asn614), but different from its counterpart in CAT (Asp199). Binding of the substrates to E2oCD is proposed to induce a change in the conformation of Asp379, allowing this residue to form a salt bridge with Arg184 that is analogous to that formed between Asp199 and Arg18 in CAT. Computer models of the active site of E2o complexed with dihydrolipoamide and with coenzyme A led to the identification of the probable succinyl-binding pocket. The residues which form this pocket (Ser330, Ser333, and His348) are probably responsible for E2o's substrate specificity.
-===CATALYTIC DOMAIN FROM DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE===
+Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex.,Knapp JE, Mitchell DT, Yazdi MA, Ernst SR, Reed LJ, Hackert ML J Mol Biol. 1998 Jul 24;280(4):655-68. PMID:9677295<ref>PMID:9677295</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1e2o" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9677295}}, adds the Publication Abstract to the page
+*[[2-oxoglutarate dehydrogenase 3D structures|2-oxoglutarate dehydrogenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9677295 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9677295}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Citric Acid Cycle]]
-E2O is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E2O OCA].
-==Reference==
-<ref group="xtra">PMID:9677295</ref><references group="xtra"/>
-[[Category: Dihydrolipoyllysine-residue succinyltransferase]]
 [[Category: Escherichia coli]]
-[[Category: Ernst, S R.]]
+[[Category: Large Structures]]
-[[Category: Hackert, M L.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Knapp, J E.]]
+[[Category: Ernst SR]]
-[[Category: Mitchell, D T.]]
+[[Category: Hackert ML]]
-[[Category: Reed, L J.]]
+[[Category: Knapp JE]]
-[[Category: Yazdi, M A.]]
+[[Category: Mitchell DT]]
-[[Category: Acyltransferase]]
+[[Category: Reed LJ]]
-[[Category: Ketoglutarate dehydrogenase multienzyme complex]]
+[[Category: Yazdi MA]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:56:40 2009''