2a00: Difference between revisions
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==The solution structure of the AMP-PNP bound nucleotide binding domain of KdpB== | ==The solution structure of the AMP-PNP bound nucleotide binding domain of KdpB== | ||
<StructureSection load='2a00' size='340' side='right' caption='[[2a00]], [[NMR_Ensembles_of_Models | 19 NMR models]]' scene=''> | <StructureSection load='2a00' size='340' side='right'caption='[[2a00]], [[NMR_Ensembles_of_Models | 19 NMR models]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2a00]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2a00]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A00 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A00 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene></td></tr> | </td></tr><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1svj|1svj]], [[1u7q|1u7q]], [[1x6k|1x6k]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1svj|1svj]], [[1u7q|1u7q]], [[1x6k|1x6k]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">kdpB ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">kdpB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Potassium-transporting_ATPase Potassium-transporting ATPase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.12 3.6.3.12] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2a00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a00 OCA], [https://pdbe.org/2a00 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a00 RCSB], [https://www.ebi.ac.uk/pdbsum/2a00 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a00 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://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] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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==See Also== | ==See Also== | ||
*[[ATPase|ATPase]] | *[[ATPase 3D structures|ATPase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Bacillus coli migula 1895]] | [[Category: Bacillus coli migula 1895]] | ||
[[Category: Large Structures]] | |||
[[Category: Potassium-transporting ATPase]] | [[Category: Potassium-transporting ATPase]] | ||
[[Category: Altendorf, K]] | [[Category: Altendorf, K]] | ||
Revision as of 11:23, 27 January 2021
The solution structure of the AMP-PNP bound nucleotide binding domain of KdpBThe solution structure of the AMP-PNP bound nucleotide binding domain of KdpB
Structural highlights
Function[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] 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 PubMedP-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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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