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1kvk

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(New page: 200px<br /><applet load="1kvk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kvk, resolution 2.40&Aring;" /> '''The Structure of Bin...)
Current revision (07:28, 14 February 2024) (edit) (undo)
 
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[[Image:1kvk.jpg|left|200px]]<br /><applet load="1kvk" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kvk, resolution 2.40&Aring;" />
 
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'''The Structure of Binary complex between a Mammalian Mevalonate Kinase and ATP: Insights into the Reaction Mechanism and Human Inherited Disease'''<br />
 
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==Overview==
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==The Structure of Binary complex between a Mammalian Mevalonate Kinase and ATP: Insights into the Reaction Mechanism and Human Inherited Disease==
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Mevalonate kinase catalyzes the ATP-dependent phosphorylation of mevalonic, acid to form mevalonate 5-phosphate, a key intermediate in the pathways of, isoprenoids and sterols. Deficiency in mevalonate kinase activity has been, linked to mevalonic aciduria and hyperimmunoglobulinemia D/periodic fever, syndrome (HIDS). The crystal structure of rat mevalonate kinase in complex, with MgATP has been determined at 2.4-A resolution. Each monomer of this, dimeric protein is composed of two domains with its active site located at, the domain interface. The enzyme-bound ATP adopts an anti conformation, in, contrast to the syn conformation reported for Methanococcus jannaschii, homoserine kinase. The Mg(2+) ion is coordinated to both beta- and, gamma-phosphates of ATP and side chains of Glu(193) and Ser(146). Asp(204), is making a salt bridge with Lys(13), which in turn interacts with the, gamma-phosphate. A model of mevalonic acid can be placed near the, gamma-phosphoryl group of ATP; thus, the C5 hydroxyl is located within 4 A, from Asp(204), Lys(13), and the gamma-phosphoryl of ATP. This arrangement, of residues strongly suggests: 1) Asp(204) abstracts the proton from C5, hydroxyl of mevalonate; 2) the penta-coordinated gamma-phosphoryl group, may be stabilized by Mg(2+), Lys(13), and Glu(193); and 3) Lys(13) is, likely to influence the pK(a) of the C5 hydroxyl of the substrate. V377I, and I268T are the most common mutations found in patients with HIDS., Val(377) is located over 18 A away from the active site and a conservative, replacement with Ile is unlikely to yield an inactive or unstable protein., Ile-268 is located at the dimer interface, and its Thr substitution may, disrupt dimer formation.
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<StructureSection load='1kvk' size='340' side='right'caption='[[1kvk]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1kvk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KVK 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]] 2.4&#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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1kvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kvk OCA], [https://pdbe.org/1kvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kvk RCSB], [https://www.ebi.ac.uk/pdbsum/1kvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kvk ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/KIME_RAT KIME_RAT] Note=Mutation in the mevalonate kinase gene causes mevalonicaciduria.
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== Function ==
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[https://www.uniprot.org/uniprot/KIME_RAT KIME_RAT] May be a regulatory site in cholesterol biosynthetic pathway.
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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/kv/1kvk_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=1kvk ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1KVK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with MG and ATP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Mevalonate_kinase Mevalonate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.36 2.7.1.36] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KVK OCA].
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*[[Mevalonate kinase|Mevalonate kinase]]
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__TOC__
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==Reference==
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</StructureSection>
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The structure of a binary complex between a mammalian mevalonate kinase and ATP: insights into the reaction mechanism and human inherited disease., Fu Z, Wang M, Potter D, Miziorko HM, Kim JJ, J Biol Chem. 2002 May 17;277(20):18134-42. Epub 2002 Feb 27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11877411 11877411]
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[[Category: Large Structures]]
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[[Category: Mevalonate kinase]]
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[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: Fu Z]]
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[[Category: Fu, Z.]]
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[[Category: Kim JJ]]
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[[Category: Kim, J.J.]]
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[[Category: Mizioko HM]]
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[[Category: Mizioko, H.M.]]
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[[Category: Potter D]]
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[[Category: Potter, D.]]
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[[Category: Wang M]]
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[[Category: Wang, M.]]
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[[Category: ATP]]
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[[Category: MG]]
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[[Category: atp]]
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[[Category: ghmp]]
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[[Category: rmk]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:55:37 2007''
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Current revision

The Structure of Binary complex between a Mammalian Mevalonate Kinase and ATP: Insights into the Reaction Mechanism and Human Inherited Disease

PDB ID 1kvk

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