2r0t

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(New page: 200px<br /><applet load="2r0t" size="350" color="white" frame="true" align="right" spinBox="true" caption="2r0t, resolution 1.9&Aring;" /> '''Crystal sructure of G...)
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[[Image:2r0t.jpg|left|200px]]<br /><applet load="2r0t" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2r0t, resolution 1.9&Aring;" />
 
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'''Crystal sructure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate geminal diamine'''<br />
 
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==Overview==
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==Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate geminal diamine==
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Di- and trideoxysugars are an important class of carbohydrates synthesized, by certain plants, fungi, and bacteria. Colitose, for example, is a, 3,6-dideoxysugar found in the O-antigens of Gram-negative bacteria such as, Escherichia coli, Salmonella enterica, Yersinia pseudotuberculosis, and, Vibrio cholerae, among others. These types of dideoxysugars are thought to, serve as antigenic determinants and to play key roles in bacterial defense, and survival. Four enzymes are required for the biochemical synthesis of, colitose starting from mannose-1-phosphate. The focus of this, investigation, GDP-4-keto-6-deoxy-d-mannose-3-dehydratase (ColD), catalyzes the third step in the pathway, namely the PLP-dependent removal, of the C3'-hydroxyl group from GDP-4-keto-6-deoxymannose. Whereas most, PLP-dependent enzymes contain an active site lysine, ColD utilizes a, histidine as its catalytic acid/base. The ping-pong mechanism of the, enzyme first involves the conversion of PLP to PMP followed by the, dehydration step. Here we present the three-dimensional structure of a, site-directed mutant form of ColD whereby the active site histidine has, been replaced with a lysine. The electron density reveals that the geminal, diamine, a tetrahedral intermediate in the formation of PMP from PLP, has, been trapped within the active site region. Functional assays further, demonstrate that this mutant form of ColD cannot catalyze the dehydration, reaction.
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<StructureSection load='2r0t' size='340' side='right'caption='[[2r0t]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2r0t]] is a 2 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=2R0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R0T FirstGlance]. <br>
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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]] 1.9&#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=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</scene></td></tr>
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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=2r0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r0t OCA], [https://pdbe.org/2r0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r0t RCSB], [https://www.ebi.ac.uk/pdbsum/2r0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r0t ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9F118_ECOLX Q9F118_ECOLX]
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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/r0/2r0t_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2r0t 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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Di- and trideoxysugars are an important class of carbohydrates synthesized by certain plants, fungi, and bacteria. Colitose, for example, is a 3,6-dideoxysugar found in the O-antigens of Gram-negative bacteria such as Escherichia coli, Salmonella enterica, Yersinia pseudotuberculosis, and Vibrio cholerae, among others. These types of dideoxysugars are thought to serve as antigenic determinants and to play key roles in bacterial defense and survival. Four enzymes are required for the biochemical synthesis of colitose starting from mannose-1-phosphate. The focus of this investigation, GDP-4-keto-6-deoxy-d-mannose-3-dehydratase (ColD), catalyzes the third step in the pathway, namely the PLP-dependent removal of the C3'-hydroxyl group from GDP-4-keto-6-deoxymannose. Whereas most PLP-dependent enzymes contain an active site lysine, ColD utilizes a histidine as its catalytic acid/base. The ping-pong mechanism of the enzyme first involves the conversion of PLP to PMP followed by the dehydration step. Here we present the three-dimensional structure of a site-directed mutant form of ColD whereby the active site histidine has been replaced with a lysine. The electron density reveals that the geminal diamine, a tetrahedral intermediate in the formation of PMP from PLP, has been trapped within the active site region. Functional assays further demonstrate that this mutant form of ColD cannot catalyze the dehydration reaction.
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==About this Structure==
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A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation.,Cook PD, Holden HM Biochemistry. 2007 Dec 11;46(49):14215-24. Epub 2007 Nov 13. PMID:17997582<ref>PMID:17997582</ref>
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2R0T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=PGU:'>PGU</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R0T OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation(,)., Cook PD, Holden HM, Biochemistry. 2007 Dec 11;46(49):14215-24. Epub 2007 Nov 13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17997582 17997582]
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</div>
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<div class="pdbe-citations 2r0t" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Cook, P.D.]]
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[[Category: Cook PD]]
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[[Category: Holden, H.M.]]
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[[Category: Holden HM]]
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[[Category: PGU]]
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[[Category: aspartate aminotransferase]]
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[[Category: colitose]]
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[[Category: geminal diamine]]
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[[Category: pyridoxal phosphate]]
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[[Category: x-ray strucutre]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:35:04 2008''
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Current revision

Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate geminal diamine

PDB ID 2r0t

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