1svj

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(New page: 200px<br /><applet load="1svj" size="450" color="white" frame="true" align="right" spinBox="true" caption="1svj" /> '''The solution structure of the nucleotide bin...)
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[[Image:1svj.gif|left|200px]]<br /><applet load="1svj" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1svj" />
 
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'''The solution structure of the nucleotide binding domain of KdpB'''<br />
 
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==Overview==
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==The solution structure of the nucleotide binding domain of KdpB==
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P-type ATPases are involved in the active transport of ions across, biological membranes. The KdpFABC complex (P-type ATPase) of Escherichia, coli is a high-affinity K+ uptake system that operates only when the cell, experiences osmotic stress or K+ limitation. Here, we present the solution, structure of the nucleotide binding domain of KdpB (backbone RMSD 0.17 A), and a model of the AMP-PNP binding mode based on intermolecular distance, restraints. The calculated AMP-PNP binding mode shows the purine ring of, the nucleotide to be "clipped" into the binding pocket via a, pi-pi-interaction to F377 on one side and a cation-pi-interaction to K395, on the other. This binding mechanism seems to be conserved in all P-type, ATPases, except the heavy metal transporting ATPases (type IB). Thus, we, conclude that the Kdp-ATPase (currently type IA) is misgrouped and has, more similarities to type III ATPases. The KdpB N-domain is the smallest, and simplest known for a P-type ATPase, and represents a minimal example, of this functional unit. No evidence of significant conformational changes, was observed within the N-domain upon nucleotide binding, thus ruling out, a role for ATP-induced conformational changes in the reaction cycle.
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<StructureSection load='1svj' size='340' side='right'caption='[[1svj]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1svj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SVJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SVJ 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">Solution NMR</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=1svj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1svj OCA], [https://pdbe.org/1svj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1svj RCSB], [https://www.ebi.ac.uk/pdbsum/1svj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1svj ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/KDPB_ECOLI KDPB_ECOLI] Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm (PubMed:2849541, PubMed:8499455, PubMed:23930894). This subunit is responsible for energy coupling to the transport system (PubMed:16354672).<ref>PMID:16354672</ref> <ref>PMID:23930894</ref> <ref>PMID:2849541</ref> <ref>PMID:8499455</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/sv/1svj_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=1svj 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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P-type ATPases are involved in the active transport of ions across biological membranes. The KdpFABC complex (P-type ATPase) of Escherichia coli is a high-affinity K+ uptake system that operates only when the cell experiences osmotic stress or K+ limitation. Here, we present the solution structure of the nucleotide binding domain of KdpB (backbone RMSD 0.17 A) and a model of the AMP-PNP binding mode based on intermolecular distance restraints. The calculated AMP-PNP binding mode shows the purine ring of the nucleotide to be "clipped" into the binding pocket via a pi-pi-interaction to F377 on one side and a cation-pi-interaction to K395 on the other. This binding mechanism seems to be conserved in all P-type ATPases, except the heavy metal transporting ATPases (type IB). Thus, we conclude that the Kdp-ATPase (currently type IA) is misgrouped and has more similarities to type III ATPases. The KdpB N-domain is the smallest and simplest known for a P-type ATPase, and represents a minimal example of this functional unit. No evidence of significant conformational changes was observed within the N-domain upon nucleotide binding, thus ruling out a role for ATP-induced conformational changes in the reaction cycle.
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==About this Structure==
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Inter-domain motions of the N-domain of the KdpFABC complex, a P-type ATPase, are not driven by ATP-induced conformational changes.,Haupt M, Bramkamp M, Coles M, Altendorf K, Kessler H J Mol Biol. 2004 Oct 1;342(5):1547-58. PMID:15364580<ref>PMID:15364580</ref>
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1SVJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Potassium-transporting_ATPase Potassium-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.12 3.6.3.12] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1SVJ 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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Inter-domain motions of the N-domain of the KdpFABC complex, a P-type ATPase, are not driven by ATP-induced conformational changes., Haupt M, Bramkamp M, Coles M, Altendorf K, Kessler H, J Mol Biol. 2004 Oct 1;342(5):1547-58. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15364580 15364580]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 1svj" style="background-color:#fffaf0;"></div>
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[[Category: Potassium-transporting ATPase]]
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[[Category: Single protein]]
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[[Category: Altendorf, K.]]
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[[Category: Bramkamp, M.]]
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[[Category: Coles, M.]]
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[[Category: Haupt, M.]]
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[[Category: Kessler, H.]]
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[[Category: alpha-beta sandwich]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:45:45 2007''
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==See Also==
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*[[ATPase 3D structures|ATPase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Altendorf K]]
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[[Category: Bramkamp M]]
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[[Category: Coles M]]
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[[Category: Haupt M]]
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[[Category: Kessler H]]

Current revision

The solution structure of the nucleotide binding domain of KdpB

PDB ID 1svj

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