1kof

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[[Image:1kof.gif|left|200px]]
 
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==Crystal structure of gluconate kinase==
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The line below this paragraph, containing "STRUCTURE_1kof", creates the "Structure Box" on the page.
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<StructureSection load='1kof' size='340' side='right'caption='[[1kof]], [[Resolution|resolution]] 2.80&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'>[[1kof]] 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=1KOF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KOF 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]] 2.8&#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=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_1kof| PDB=1kof | 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=1kof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kof OCA], [https://pdbe.org/1kof PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kof RCSB], [https://www.ebi.ac.uk/pdbsum/1kof PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kof ProSAT]</span></td></tr>
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</table>
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'''Crystal structure of gluconate kinase'''
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== Function ==
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[https://www.uniprot.org/uniprot/GNTK_ECOLI GNTK_ECOLI]
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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The crystal structure of gluconate kinase from Escherichia coli has been determined to 2.0 A resolution by X-ray crystallography. The three-dimensional structure was solved by multi-wavelength anomalous dispersion, using a crystal of selenomethionine-substituted enzyme. Gluconate kinase is an alpha/beta structure consisting of a twisted parallel beta-sheet surrounded by alpha-helices with overall topology similar to nucleoside monophosphate (NMP) kinases, such as adenylate kinase. In order to identify residues involved in substrate binding and catalysis, structures of binary complexes with ATP, the ATP analogue adenosine 5'-(beta,gamma-methylene) triphosphate and the product, gluconate-6-phosphate have been determined. Significant conformational changes are induced upon binding of ATP to the enzyme. The largest changes involve a hinge-bending motion of the NMP(bind) part and a motion of the LID with adjacent helices, which opens the cavity to the second substrate, gluconate. Opening of the active site cleft upon ATP binding is the opposite of what has been observed in the NMP kinase family so far, which usually close their active site to prevent fortuitous hydrolysis of ATP. The conformational change positions the side-chain of Arg120 to stack with the purine ring of ATP and the side-chain of Arg124 is shifted to interact with the alpha-phosphate in ATP, at the same time protecting ATP from solvent water. The beta and gamma-phosphate groups of ATP bind in the predicted P-loop. A conserved lysine side-chain interacts with the gamma-phosphate group, and might promote phosphoryl transfer. Gluconate-6-phosphate binds with its phosphate group in a similar position as the gamma-phosphate of ATP, consistent with inline phosphoryl transfer. The gluconate binding-pocket in GntK is located in a different position than the nucleoside binding-site usually found in NMP kinases.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ko/1kof_consurf.spt"</scriptWhenChecked>
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1KOF is a [[Single protein]] 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=1KOF OCA].
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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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==Reference==
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</jmolCheckbox>
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Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography., Kraft L, Sprenger GA, Lindqvist Y, J Mol Biol. 2002 May 10;318(4):1057-69. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12054802 12054802]
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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=1kof ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Gluconokinase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Kraft L]]
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[[Category: Kraft, L.]]
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[[Category: Lindqvist Y]]
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[[Category: Lindqvist, Y.]]
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[[Category: Sprenger GA]]
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[[Category: Sprenger, G A.]]
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[[Category: Alfa/beta]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 22:58:57 2008''
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Current revision

Crystal structure of gluconate kinase

PDB ID 1kof

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