4K0D | pdb_00004k0d

Periplasmic sensor domain of sensor histidine kinase, Adeh_2942

• PDB DOI: https://doi.org/10.2210/pdb4K0D/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Anaeromyxobacter dehalogenans 2CP-C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-03 Released: 2013-06-12 
• Deposition Author(s): Pokkuluri, P.R., Mack, J.C., Bearden, J., Rakowski, E., Schiffer, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.252 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Analysis of periplasmic sensor domains from Anaeromyxobacter dehalogenans 2CP-C: structure of one sensor domain from a histidine kinase and another from a chemotaxis protein.

Pokkuluri, P.R., Dwulit-Smith, J., Duke, N.E., Wilton, R., Mack, J.C., Bearden, J., Rakowski, E., Babnigg, G., Szurmant, H., Joachimiak, A., Schiffer, M.

(2013) Microbiologyopen 2: 766-777

• PubMed: 23897711 
• DOI: https://doi.org/10.1002/mbo3.112
• Primary Citation Related Structures: 
  4K08, 4K0D


• PubMed Abstract: 
  

  Anaeromyxobacter dehalogenans is a δ-proteobacterium found in diverse soils and sediments. It is of interest in bioremediation efforts due to its dechlorination and metal-reducing capabilities. To gain an understanding on A. dehalogenans' abilities to adapt to diverse environments we analyzed its signal transduction proteins. The A. dehalogenans genome codes for a large number of sensor histidine kinases (HK) and methyl-accepting chemotaxis proteins (MCP); among these 23 HK and 11 MCP proteins have a sensor domain in the periplasm. These proteins most likely contribute to adaptation to the organism's surroundings. We predicted their three-dimensional folds and determined the structures of two of the periplasmic sensor domains by X-ray diffraction. Most of the domains are predicted to have either PAS-like or helical bundle structures, with two predicted to have solute-binding protein fold, and another predicted to have a 6-phosphogluconolactonase like fold. Atomic structures of two sensor domains confirmed the respective fold predictions. The Adeh_2942 sensor (HK) was found to have a helical bundle structure, and the Adeh_3718 sensor (MCP) has a PAS-like structure. Interestingly, the Adeh_3718 sensor has an acetate moiety bound in a binding site typical for PAS-like domains. Future work is needed to determine whether Adeh_3718 is involved in acetate sensing by A. dehalogenans.

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Organizational Affiliation: 
• Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois, 60439.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.06 kDa 
• Atom Count: 2,290 
• Modeled Residue Count: 288 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic sensor hybrid histidine kinase	A, B	152	Anaeromyxobacter dehalogenans 2CP-C	Mutation(s): 0  Gene Names: Adeh_2942 EC: 2.7.13.3
UniProt
Find proteins for Q2IDQ5 (Anaeromyxobacter dehalogenans (strain 2CP-C)) Explore Q2IDQ5  Go to UniProtKB:  Q2IDQ5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	M [auth B], N [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	E [auth A], F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.252 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.693	α = 90
b = 75.184	β = 105.18
c = 51.031	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-12 
Deposition Author(s): Pokkuluri, P.R., Mack, J.C., Bearden, J., Rakowski, E., Schiffer, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Structure summary
• Version 1.2: 2015-04-15
  Changes: Database references
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary