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1kof

From Proteopedia

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[[Image:1kof.gif|left|200px]]
 
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{{Structure
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==Crystal structure of gluconate kinase==
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|PDB= 1kof |SIZE=350|CAPTION= <scene name='initialview01'>1kof</scene>, resolution 2.80&Aring;
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<StructureSection load='1kof' size='340' side='right'caption='[[1kof]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
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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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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Gluconokinase Gluconokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.12 2.7.1.12] </span>
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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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|GENE= gntk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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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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|DOMAIN=
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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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|RELATEDENTRY=[[1knq|1KNQ]], [[1ko1|1KO1]], [[1ko4|1KO4]], [[1ko5|1KO5]], [[1ko8|1KO8]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kof OCA], [http://www.ebi.ac.uk/pdbsum/1kof PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kof RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/GNTK_ECOLI GNTK_ECOLI]
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== Evolutionary Conservation ==
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'''Crystal structure of gluconate kinase'''
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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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==Overview==
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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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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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<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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==About this Structure==
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</jmolCheckbox>
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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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</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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==Reference==
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__TOC__
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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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</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 Sun Mar 30 21:51:21 2008''
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Current revision

Crystal structure of gluconate kinase

PDB ID 1kof

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