3hww

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{{Seed}}
 
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[[Image:3hww.jpg|left|200px]]
 
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==Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate==
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The line below this paragraph, containing "STRUCTURE_3hww", creates the "Structure Box" on the page.
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<StructureSection load='3hww' size='340' side='right'caption='[[3hww]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3hww]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HWW FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_3hww| PDB=3hww | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hww OCA], [https://pdbe.org/3hww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hww RCSB], [https://www.ebi.ac.uk/pdbsum/3hww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hww ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MEND_ECOLI MEND_ECOLI] Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC).<ref>PMID:1459959</ref> <ref>PMID:17760421</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hw/3hww_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=3hww ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Here we describe in detail the crystal structures of the Vitamin K(2) synthesis protein MenD, from Escherichia coli, in complex with thiamine diphosphate (ThDP) and oxoglutarate, and the effects of cofactor and substrate on its structural stability. This is the first reported structure of MenD in complex with oxoglutarate. The residues Gly472 to Phe488 of the active site region are either disordered, or in an open conformation in the MenD oxoglutarate complex structure, but adopt a closed conformation in the MenD ThDP complex structure. Biospecific-interaction analysis using surface plasmon resonance (SPR) technology reveals an affinity for ThDP and oxoglutarate in the nanomolar range. Biochemical and structural analysis confirmed that MenD is highly dependent on ThDP for its structural stability. Our structural results combined with the biochemical assay reveal novel features of the enzyme that could be utilized in a program of rational structure-based drug design, as well as in helping to enhance our knowledge of the menaquinone synthesis pathway in greater detail.
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===Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate===
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Structural and functional analysis of Vitamin K2 synthesis protein MenD.,Priyadarshi A, Kim EE, Hwang KY Biochem Biophys Res Commun. 2009 Oct 30;388(4):748-51. Epub 2009 Aug 22. PMID:19703421<ref>PMID:19703421</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19703421}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3hww" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19703421 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19703421}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia coli K-12]]
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3HWW is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWW OCA].
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[[Category: Large Structures]]
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[[Category: Hwang KY]]
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==Reference==
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[[Category: Priyadarshi A]]
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<ref group="xtra">PMID:19703421</ref><references group="xtra"/>
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[[Category: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase]]
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[[Category: Escherichia coli k-12]]
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[[Category: Hwang, K Y.]]
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[[Category: Priyadarshi, A.]]
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[[Category: Carboxylase]]
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[[Category: Magnesium]]
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[[Category: Manganese]]
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[[Category: Menaquinone]]
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[[Category: Menaquinone biosynthesis]]
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[[Category: Metal]]
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[[Category: Metal-binding]]
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[[Category: Mg]]
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[[Category: Thdp]]
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[[Category: Thiamine pyrophosphate]]
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[[Category: Transferase]]
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[[Category: Vitamin k2]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 4 10:58:57 2009''
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Current revision

Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate

PDB ID 3hww

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