Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.89 kDa 
• Atom Count: 1311 
• Modelled Residue Count: 133 
• Deposited Residue Count: 142 
• Unique protein chains: 1

3BY8

Crystal Structure of the E.coli DcuS Sensor Domain

• DOI: 10.2210/pdb3BY8/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-15 Released: 2008-08-12 
• Deposition Author(s): Cheung, J., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.232 
• R-Value Work: 0.219 

Literature

Crystal Structures of C4-Dicarboxylate Ligand Complexes with Sensor Domains of Histidine Kinases DcuS and DctB.

Cheung, J., Hendrickson, W.A.

(2008) J Biol Chem 283: 30256-30265

• PubMed: 18701447 
• DOI: 10.1074/jbc.M805253200
• Primary Citation of Related Structures:  
  3BY8, 3BY9


• PubMed Abstract: 
  

Two-component signaling systems allow bacteria to adapt to changing environments. Typically, a chemical or other stimulus is detected by the periplasmic sensor domain of a transmembrane histidine kinase sensor, which in turn relays a signal through a phosphotransfer cascade to the cognate cytoplasmic response regulator. Such systems lead ultimately to changes in gene expression or cell motility. Mechanisms of ligand binding and signal transduction through the cell membrane in histidine kinases are not fully understood. In an effort to further understand such processes, we have solved the crystal structures of the periplasmic sensor domains of Escherichia coli DcuS and of Vibrio cholerae DctB in complex with the respective cognate ligands, malate and succinate. Both proteins are involved in the regulation of the transport and metabolism of C(4)-dicarboxylates, but they are not highly related by sequence similarity. Our work reveals that despite disparate sizes, both structures contain a similar characteristic alpha/beta PDC (PhoQ-DcuS-CitA) sensor-domain fold and display similar modes of ligand binding, suggesting similar mechanisms of function.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein dcuS	A	142	Escherichia coli	Mutation(s): 0  Gene Names: dcuS, yjdH EC: 2.7.13.3
Find proteins for P0AEC8 (Escherichia coli (strain K12)) Explore P0AEC8  Go to UniProtKB:  P0AEC8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMR	B [auth A]	(2S)-2-hydroxybutanedioic acid C4 H6 O5 BJEPYKJPYRNKOW-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.232 
• R-Value Work: 0.219 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.111	α = 90
b = 86.111	β = 90
c = 35.207	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-15 
• Released Date: 2008-08-12 
Deposition Author(s): Cheung, J., Hendrickson, W.A.

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 2.0: 2021-04-21
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary