Structure and function of the juxtamembrane GAF domain of potassium biosensor KdpD

Abstract

KdpD/KdpE two‐component signaling system regulates expression of a high affinity potassium transporter responsible for potassium homeostasis. The C‐terminal module of KdpD consists of a GAF domain linked to a histidine kinase domain. Whereas certain GAF domains act as regulators by binding cyclic nucleotides, the role of the juxtamembrane GAF domain in KdpD is unknown. We report the high‐resolution crystal structure of KdpD GAF domain (KdpDG) consisting of five α‐helices, four β‐sheets and two large loops. KdpDG forms a symmetry‐related dimer, wherein parallelly arranged monomers contribute to a four‐helix bundle at the dimer‐interface, SAXS analysis of KdpD C‐terminal module reveals an elongated structure that is a dimer in solution. Substitution of conserved residues with various residues that disrupt the dimer interface produce a range of effects on gene expression demonstrating the importance of the interface in inactive to active transitions during signaling. Comparison of ligand binding site of the classic cyclic nucleotide‐binding GAF domains to KdpDG reveals structural differences arising from naturally occurring substitutions in primary sequence of KdpDG that modifies the canonical NKFDE sequence motif required for cyclic nucleotide binding. Together these results suggest a structural role for KdpDG in dimerization and transmission of signal to the kinase domain.

Structural basis of KdpD histidine kinase binding to the second messenger c-di-AMP

“…The c-di-AMP-bound USP Sa structure presented here completes the structural repertoire for all of the individual domains in the KdpDE two-component system (43)(44)(45). However, it is yet to be determined how this two-component system's function is regulated by the binding of c-di-AMP to KdpD in Firmicutes.…”

“…The histidine kinase domain of KdpD acts as a kinase and a phosphatase to the response regulator transcription factor KdpE, and regulates >100 genes governing potassium homeostasis, capsule synthesis, and virulence in S. aureus ( 35 ). The structures of the canonical transmembrane domain ( 41 ), the GAF domain ( 42 ), the KdpD domain (Protein Data Bank ID: 2R8R ), and the KdpE-bound histidine kinase domains ( 43 ) are known. The structure of the USP domain in the N-terminal region complexed to c-di-AMP (highlighted by a box with a red dotted border ) has been determined in this study.…”

“…While the structures of rest of the domains in KdpD are known ( Fig. 1 A ) ( 41 , 42 , 43 ), the lack of knowledge concerning the three-dimensional structure of the USP in KdpD-NTR (USP KdpD ) limits our understanding of its function. USP KdpD belongs to a more widespread USP family of proteins (∼15 kDa), with members ubiquitously produced by all kingdoms of life ( 44 ).…”

Regulation of potassium homeostasis inCaulobacter crescentus

“…Comparison of Pfam features highlighted that the KdpD sequence of C. crescentus lacks the cytoplasmic GAF domain known to be linked to the DHp domain in E. coli (44) (Fig. 8D).…”

Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity

“… Structural models of different GAF domains: homology models of NarQ and NarX GAF-like domains, which are based on the structure of the Acinetobacter baylyi phosphoenolpyruvate-protein phosphotransferase (ptsP) GAF domain (PDB ID 3CI6); E. coli potassium sensor HK KdpD GAF domain (PDB ID 4QPR [ 202 ]); phycocyanobilin-bound Leptolyngbya sp. JSC-1 phosphorylation-responsive photosensitive histidine kinase (PPHK) GAF domain (PDB ID 6OAP, [ 203 ]); cyclic AMP-bound Anabaena adenylyl cyclase cyaB2 GAF domain (PDB ID 1YKD [ 204 ]).…”