1svj: Difference between revisions

Revision as of 16:05, 21 February 2008

The solution structure of the nucleotide binding domain of KdpB

OverviewOverview

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.

About this StructureAbout this Structure

1SVJ is a Single protein structure of sequence from Escherichia coli. Active as Potassium-transporting ATPase, with EC number 3.6.3.12 Full crystallographic information is available from OCA.

ReferenceReference

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

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OCA

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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" />
 '''The solution structure of the nucleotide binding domain of KdpB'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-SVJ 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].
+SVJ 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1SVJ OCA].
 ==Reference==
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 [[Category: alpha-beta sandwich]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:45:45 2007''
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