2a29: Difference between revisions

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-[[Image:2a29.png|left|200px]]
-<!--
+==The solution structure of the AMP-PNP bound nucleotide binding domain of KdpB==
-The line below this paragraph, containing "STRUCTURE_2a29", creates the "Structure Box" on the page.
+<StructureSection load='2a29' size='340' side='right'caption='[[2a29]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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='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>
-{{STRUCTURE_2a29|  PDB=2a29  |  SCENE=  }}
+<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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16354672}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2a29" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16354672 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_16354672}}
-==About this Structure==
-[[2a29]] is a 1 chain structure of [[ATPase]] with sequence from [http://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].
 ==See Also==
-*[[ATPase]]
+*[[ATPase 3D structures|ATPase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:16354672</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[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]]
-[[Category: Hydrolase]]