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| - | [[Image:2a29.gif|left|200px]] | |
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| - | {{Structure
| + | ==The solution structure of the AMP-PNP bound nucleotide binding domain of KdpB== |
| - | |PDB= 2a29 |SIZE=350|CAPTION= <scene name='initialview01'>2a29</scene>
| + | <StructureSection load='2a29' size='340' side='right'caption='[[2a29]]' scene=''> |
| - | |SITE= | + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER'>ANP</scene> | + | <table><tr><td colspan='2'>[[2a29]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1x6k 1x6k]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A29 FirstGlance]. <br> |
| - | |ACTIVITY= [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]
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | |GENE= KDPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene></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=2a29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a29 OCA], [https://pdbe.org/2a29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a29 RCSB], [https://www.ebi.ac.uk/pdbsum/2a29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a29 ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [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 == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a2/2a29_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </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/main_output.php?pdb_ID=2a29 ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | P-type ATPases are ubiquitously abundant enzymes involved in active transport of charged residues across biological membranes. The KdpB subunit of the prokaryotic Kdp-ATPase (KdpFABC complex) shares characteristic regions of homology with class II-IV P-type ATPases and has been shown previously to be misgrouped as a class IA P-type ATPase. Here, we present the NMR structure of the AMP-PNP-bound nucleotide binding domain KdpBN of the Escherichia coli Kdp-ATPase at high resolution. The aromatic moiety of the nucleotide is clipped into the binding pocket by Phe(377) and Lys(395) via a pi-pi stacking and a cation-pi interaction, respectively. Charged residues at the outer rim of the binding pocket (Arg(317), Arg(382), Asp(399), and Glu(348)) stabilize and direct the triphosphate group via electrostatic attraction and repulsion toward the phosphorylation domain. The nucleotide binding mode was corroborated by the replacement of critical residues. The conservative mutation F377Y produced a high residual nucleotide binding capacity, whereas replacement by alanine resulted in low nucleotide binding capacities and a considerable loss of ATPase activity. Similarly, mutation K395A resulted in loss of ATPase activity and nucleotide binding affinity, even though the protein was properly folded. We present a schematic model of the nucleotide binding mode that allows for both high selectivity and a low nucleotide binding constant, necessary for the fast and effective turnover rate realized in the reaction cycle of the Kdp-ATPase. |
| | | | |
| - | '''The solution structure of the AMP-PNP bound nucleotide binding domain of KdpB'''
| + | The holo-form of the nucleotide binding domain of the KdpFABC complex from Escherichia coli reveals a new binding mode.,Haupt M, Bramkamp M, Heller M, Coles M, Deckers-Hebestreit G, Herkenhoff-Hesselmann B, Altendorf K, Kessler H J Biol Chem. 2006 Apr 7;281(14):9641-9. Epub 2005 Dec 14. PMID:16354672<ref>PMID:16354672</ref> |
| | | | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 2a29" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Overview== | + | ==See Also== |
| - | P-type ATPases are ubiquitously abundant enzymes involved in active transport of charged residues across biological membranes. The KdpB subunit of the prokaryotic Kdp-ATPase (KdpFABC complex) shares characteristic regions of homology with class II-IV P-type ATPases and has been shown previously to be misgrouped as a class IA P-type ATPase. Here, we present the NMR structure of the AMP-PNP-bound nucleotide binding domain KdpBN of the Escherichia coli Kdp-ATPase at high resolution. The aromatic moiety of the nucleotide is clipped into the binding pocket by Phe(377) and Lys(395) via a pi-pi stacking and a cation-pi interaction, respectively. Charged residues at the outer rim of the binding pocket (Arg(317), Arg(382), Asp(399), and Glu(348)) stabilize and direct the triphosphate group via electrostatic attraction and repulsion toward the phosphorylation domain. The nucleotide binding mode was corroborated by the replacement of critical residues. The conservative mutation F377Y produced a high residual nucleotide binding capacity, whereas replacement by alanine resulted in low nucleotide binding capacities and a considerable loss of ATPase activity. Similarly, mutation K395A resulted in loss of ATPase activity and nucleotide binding affinity, even though the protein was properly folded. We present a schematic model of the nucleotide binding mode that allows for both high selectivity and a low nucleotide binding constant, necessary for the fast and effective turnover rate realized in the reaction cycle of the Kdp-ATPase.
| + | *[[ATPase 3D structures|ATPase 3D structures]] |
| - | | + | == References == |
| - | ==About this Structure== | + | <references/> |
| - | 2A29 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry 1X6K. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A29 OCA].
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==Reference==
| + | |
| - | The holo-form of the nucleotide binding domain of the KdpFABC complex from Escherichia coli reveals a new binding mode., Haupt M, Bramkamp M, Heller M, Coles M, Deckers-Hebestreit G, Herkenhoff-Hesselmann B, Altendorf K, Kessler H, J Biol Chem. 2006 Apr 7;281(14):9641-9. Epub 2005 Dec 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16354672 16354672]
| + | |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Potassium-transporting ATPase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[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: ANP]]
| + | |
| - | [[Category: alpha-beta sandwich]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:44:29 2008''
| + | |
| 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 ubiquitously abundant enzymes involved in active transport of charged residues across biological membranes. The KdpB subunit of the prokaryotic Kdp-ATPase (KdpFABC complex) shares characteristic regions of homology with class II-IV P-type ATPases and has been shown previously to be misgrouped as a class IA P-type ATPase. Here, we present the NMR structure of the AMP-PNP-bound nucleotide binding domain KdpBN of the Escherichia coli Kdp-ATPase at high resolution. The aromatic moiety of the nucleotide is clipped into the binding pocket by Phe(377) and Lys(395) via a pi-pi stacking and a cation-pi interaction, respectively. Charged residues at the outer rim of the binding pocket (Arg(317), Arg(382), Asp(399), and Glu(348)) stabilize and direct the triphosphate group via electrostatic attraction and repulsion toward the phosphorylation domain. The nucleotide binding mode was corroborated by the replacement of critical residues. The conservative mutation F377Y produced a high residual nucleotide binding capacity, whereas replacement by alanine resulted in low nucleotide binding capacities and a considerable loss of ATPase activity. Similarly, mutation K395A resulted in loss of ATPase activity and nucleotide binding affinity, even though the protein was properly folded. We present a schematic model of the nucleotide binding mode that allows for both high selectivity and a low nucleotide binding constant, necessary for the fast and effective turnover rate realized in the reaction cycle of the Kdp-ATPase.
The holo-form of the nucleotide binding domain of the KdpFABC complex from Escherichia coli reveals a new binding mode.,Haupt M, Bramkamp M, Heller M, Coles M, Deckers-Hebestreit G, Herkenhoff-Hesselmann B, Altendorf K, Kessler H J Biol Chem. 2006 Apr 7;281(14):9641-9. Epub 2005 Dec 14. PMID:16354672[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, 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
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