1SVJ: The solution structure of the nucleotide binding domain of KdpB

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.
PDB ID: 1SVJDownload
MMDB ID: 29382
PDB Deposition Date: 2004/3/29
Updated in MMDB: 2007/11
Experimental Method:
solution nmr
Source Organism:
Similar Structures:
Molecular Components in 1SVJ
Label Count Molecule
Protein (1 molecule)
Potassium-transporting Atpase B Chain(Gene symbol: kdpB)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB