1eq2: Difference between revisions

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-[[Image:1eq2.png|left|200px]]
-{{STRUCTURE_1eq2|  PDB=1eq2  |  SCENE=  }}
+==THE CRYSTAL STRUCTURE OF ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE==
+<StructureSection load='1eq2' size='340' side='right'caption='[[1eq2]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1eq2]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EQ2 FirstGlance]. <br>
+</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=ADQ:ADENOSINE-5-DIPHOSPHATE-GLUCOSE'>ADQ</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></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=1eq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eq2 OCA], [https://pdbe.org/1eq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eq2 RCSB], [https://www.ebi.ac.uk/pdbsum/1eq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eq2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HLDD_ECOLI HLDD_ECOLI] Catalyzes the interconversion between ADP-D-glycero-beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose via an epimerization at carbon 6 of the heptose.<ref>PMID:6337148</ref>
+== 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/eq/1eq2_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=1eq2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: ADP-L-glycero--mannoheptose 6-epimerase (AGME) is required for lipopolysaccharide (LPS) biosynthesis in most genera of pathogenic and non-pathogenic Gram-negative bacteria. It catalyzes the interconversion of ADP-D-glycero-D-mannoheptose and ADP-L-glycero-D-mannoheptose, a precursor of the seven-carbon sugar L-glycero-mannoheptose (heptose). Heptose is an obligatory component of the LPS core domain; its absence results in a truncated LPS structure resulting in susceptibility to hydrophobic antibiotics. Heptose is not found in mammalian cells, thus its biosynthetic pathway in bacteria presents a unique target for the design of novel antimicrobial agents. RESULTS: The structure of AGME, in complex with NADP and the catalytic inhibitor ADP-glucose, has been determined at 2.0 A resolution by multiwavelength anomalous diffraction (MAD) phasing methods. AGME is a homopentameric enzyme, which crystallizes with two pentamers in the asymmetric unit. The location of 70 crystallographically independent selenium sites was a key step in the structure determination process. Each monomer comprises two domains: a large N-terminal domain, consisting of a modified seven-stranded Rossmann fold that is associated with NADP binding; and a smaller alpha/beta C-terminal domain involved in substrate binding. CONCLUSIONS: The first structure of an LPS core biosynthetic enzyme leads to an understanding of the mechanism of the conversion between ADP-D-glycero--mannoheptose and ADP-L-glycero-D-mannoheptose. On the basis of its high structural similarity to UDP-galactose epimerase and the three-dimensional positions of the conserved residues Ser116, Tyr140 and Lys144, AGME was classified as a member of the short-chain dehydrogenase/reductase (SDR) superfamily. This study should prove useful in the design of mechanistic and structure-based inhibitors of the AGME catalyzed reaction.
-===THE CRYSTAL STRUCTURE OF ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE===
+The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist.,Deacon AM, Ni YS, Coleman WG Jr, Ealick SE Structure. 2000 May 15;8(5):453-62. PMID:10896473<ref>PMID:10896473</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-[[1eq2]] is a 10 chain structure with 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=1EQ2 OCA].
+<div class="pdbe-citations 1eq2" style="background-color:#fffaf0;"></div>
+== References ==
-==See Also==
+<references/>
-*[[InhA|InhA]]
+__TOC__
+</StructureSection>
-==Reference==
-<ref group="xtra">PMID:010896473</ref><references group="xtra"/>
-[[Category: ADP-glyceromanno-heptose 6-epimerase]]
 [[Category: Escherichia coli]]
-[[Category: Coleman, W G.]]
+[[Category: Large Structures]]
-[[Category: Deacon, A M.]]
+[[Category: Coleman Jr WG]]
-[[Category: Ealick, S E.]]
+[[Category: Deacon AM]]
-[[Category: Ni, Y S.]]
+[[Category: Ealick SE]]
-[[Category: C-terminal mixed alpha/beta domain]]
+[[Category: Ni YS]]
-[[Category: Isomerase]]
-[[Category: N-terminal domain rossmann fold]]
-[[Category: Short-chain dehydrogenase/reductase fold]]