1SVJ

The solution structure of the nucleotide binding domain of KdpB

Summary for 1SVJ

• Entry DOI: 10.2210/pdb1svj/pdb
• Related: 1U7Q 1X6K
• NMR Information: BMRB: 6029
• Descriptor: Potassium-transporting ATPase B chain (1 entity in total)
• Functional Keywords: alpha-beta sandwich, hydrolase
• Biological source: Escherichia coli
• Cellular location: Cell inner membrane; Multi-pass membrane protein: P03960
• Total number of polymer chains: 1
• Total formula weight: 17168.30

Authors

Haupt, M.,Bramkamp, M.,Coles, M.,Altendorf, K.,Kessler, H. (deposition date: 2004-03-29, release date: 2004-09-21, Last modification date: 2024-05-22)

Primary citation

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., 342:1547-1558, 2004

PubMed Abstract: 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.

PubMed: 15364580
DOI: 10.1016/j.jmb.2004.07.060

Experimental method

SOLUTION NMR