PDBsum entry 3ehh

Transferase

PDB id: 3ehh

Contents

Protein chains

192 a.a. *

Ligands

ADP ×2

Metals

_CA ×2

Waters ×103

* Residue conservation analysis

PDB id:

3ehh

Name:

Transferase

Title:

Crystal structure of deskc-h188v in complex with adp

Structure:

Sensor kinase (yocf protein). Chain: a, b. Fragment: entire cytoplasmic region. Synonym: desk histidine kinase. Engineered: yes. Mutation: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: yocf. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.10Å R-factor: 0.195 R-free: 0.232

Authors:

D.Albanesi,P.M.Alzari,A.Buschiazzo

Key ref:

D.Albanesi et al. (2009). Structural plasticity and catalysis regulation of a thermosensor histidine kinase. Proc Natl Acad Sci U S A, 106, 16185-16190. PubMed id: 19805278 DOI: 10.1073/pnas.0906699106

Date:

12-Sep-08 Release date: 15-Sep-09

Protein chains

O34757  (DESK_BACSU) -  Sensor histidine kinase DesK from Bacillus subtilis (strain 168)

Seq: 370 a.a.

Struc: 192 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.13.3 - histidine kinase.
• Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine

ATP + protein L-histidine = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + protein N-phospho-L-histidine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0906699106

Proc Natl Acad Sci U S A 106:16185-16190 (2009)

PubMed id: 19805278

Structural plasticity and catalysis regulation of a thermosensor histidine kinase.

D.Albanesi, M.Martín, F.Trajtenberg, M.C.Mansilla, A.Haouz, P.M.Alzari, D.de Mendoza, A.Buschiazzo.

ABSTRACT

Temperature sensing is essential for the survival of living cells. A major challenge is to understand how a biological thermometer processes thermal information to optimize cellular functions. Using structural and biochemical approaches, we show that the thermosensitive histidine kinase, DesK, from Bacillus subtilis is cold-activated through specific interhelical rearrangements in its central four-helix bundle domain. As revealed by the crystal structures of DesK in different functional states, the plasticity of this helical domain influences the catalytic activities of the protein, either by modifying the mobility of the ATP-binding domains for autokinase activity or by modulating binding of the cognate response regulator to sustain the phosphotransferase and phosphatase activities. The structural and biochemical data suggest a model in which the transmembrane sensor domain of DesK promotes these structural changes through conformational signals transmitted by the membrane-connecting two-helical coiled-coil, ultimately controlling the alternation between output autokinase and phosphatase activities. The structural comparison of the different DesK variants indicates that incoming signals can take the form of helix rotations and asymmetric helical bends similar to those reported for other sensing systems, suggesting that a similar switching mechanism could be operational in a wide range of sensor histidine kinases.

Selected figure(s)

Figure 1.
Three distinct conformational states of DesKC. Cartoon representations of the DesK homodimers, with the two [alpha]-helical hairpins from the DHp domain highlighted in pink ([alpha]1) and blue ([alpha]2), the ABDs colored in yellow, and bound nucleotides in green. (A) Overall structures of DesKC[[Delta]174] (Top) and E188b (Bottom), with mobile ABDs. (B) Structure of DesKC-P (Top), similar to E188a (Bottom), rotated approximately 60[deg] around the vertical axis with respect to (A) for clarity. (C) Structures of V188a (Top) and V188b (Bottom). (D) Superposition of the 11 independent ABDs seen in all DesKC variants. The bound nucleotide is shown in cyan, with the adenine ring stacked against F324 (in yellow). The Mg^2+ ion (in red) contacts the nucleotide phosphates and two residues (E289 and N293, in green) that belong to the conserved N box (17). The ATP-lid (residues 321 --334) shows the largest structural differences and is partially disordered in many crystal structures. (E) Hydrophobic residues (CPK spheres) of one helical hairpin that, upon dimerization, forms the core of the 4-HB in DesKC[[Delta]174]. For each residue, its a/d position within the heptad repeats and the percentage of members of the HisKA_3 subfamily having a hydrophobic residue (AVLMI) at the same position are indicated in parenthesis.

Figure 3.
Extensive intradomain interactions in DesKC[H188V]. (A) Close view of the interaction between the ABDs and the DHp domain in DesKC[H188V]. Key residues are colored according to the type of interaction (electrostatic in red, hydrophobic in blue, and H-bonding in green). (B) Cartoon representation (Right) of the two-helical coiled-coil formed by the homodimerization of residues 160 --180. Core hydrophobic residues are shown in stick representation. Molecular surface representation (Left) of the same helical region for one monomer, showing the exposed hydrophobic patch. (C) Overall view of the parallel coiled-coil and the 4-HB in DesKC[H188V]. The molecular surface color-coded according to electrostatic charges is shown for helix [alpha]1 in one monomer. The side-chains of I183 and L187, which were part of the DHp core in DesKC[[Delta]174], are now at the outer surface of the domain (engaged in interactions with the ABD domain, not shown).

Figures were selected by an automated process.