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| | ==The solution structure of the nucleotide binding domain of KdpB== | | ==The solution structure of the nucleotide binding domain of KdpB== |
| - | <StructureSection load='1svj' size='340' side='right' caption='[[1svj]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''> | + | <StructureSection load='1svj' size='340' side='right'caption='[[1svj]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1svj]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SVJ FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1u7q|1u7q]], [[1x6k|1x6k]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KDPB, B0697 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
| + | <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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1svj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1svj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1svj RCSB], [http://www.ebi.ac.uk/pdbsum/1svj PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ATKB_ECOLI ATKB_ECOLI]] One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions.[HAMAP-Rule:MF_00285] | + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sv/1svj_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sv/1svj_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| - | </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/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </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]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 1svj" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[ATPase|ATPase]] | + | *[[ATPase 3D structures|ATPase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Potassium-transporting ATPase]] | + | [[Category: Large Structures]] |
| - | [[Category: Altendorf, K]] | + | [[Category: Altendorf K]] |
| - | [[Category: Bramkamp, M]] | + | [[Category: Bramkamp M]] |
| - | [[Category: Coles, M]] | + | [[Category: Coles M]] |
| - | [[Category: Haupt, M]] | + | [[Category: Haupt M]] |
| - | [[Category: Kessler, H]] | + | [[Category: Kessler H]] |
| - | [[Category: Alpha-beta sandwich]]
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| - | [[Category: Hydrolase]]
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| Structural highlights
Function
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).[1] [2] [3] [4]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Haupt M, Bramkamp M, Heller M, Coles M, Deckers-Hebestreit G, Herkenhoff-Hesselmann B, Altendorf K, Kessler H. The holo-form of the nucleotide binding domain of the KdpFABC complex from Escherichia coli reveals a new binding mode. J Biol Chem. 2006 Apr 7;281(14):9641-9. Epub 2005 Dec 14. PMID:16354672 doi:http://dx.doi.org/10.1074/jbc.M508290200
- ↑ Damnjanovic B, Weber A, Potschies M, Greie JC, Apell HJ. Mechanistic analysis of the pump cycle of the KdpFABC P-type ATPase. Biochemistry. 2013 Aug 20;52(33):5563-76. doi: 10.1021/bi400729e. Epub 2013 Aug, 9. PMID:23930894 doi:http://dx.doi.org/10.1021/bi400729e
- ↑ Siebers A, Altendorf K. The K+-translocating Kdp-ATPase from Escherichia coli. Purification, enzymatic properties and production of complex- and subunit-specific antisera. Eur J Biochem. 1988 Dec 1;178(1):131-40. PMID:2849541
- ↑ Kollmann R, Altendorf K. ATP-driven potassium transport in right-side-out membrane vesicles via the Kdp system of Escherichia coli. Biochim Biophys Acta. 1993 Jun 10;1143(1):62-6. PMID:8499455
- ↑ Haupt M, Bramkamp M, Coles M, Altendorf K, Kessler H. Inter-domain motions of the N-domain of the KdpFABC complex, a P-type ATPase, are not driven by ATP-induced conformational changes. J Mol Biol. 2004 Oct 1;342(5):1547-58. PMID:15364580 doi:http://dx.doi.org/10.1016/j.jmb.2004.07.060
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