Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 546.97 kDa 
• Atom Count: 35839 
• Modelled Residue Count: 4478 
• Deposited Residue Count: 4770 
• Unique protein chains: 1

4A2L

Structure of the periplasmic domain of the heparin and heparan sulphate sensing hybrid two component system BT4663 in apo and ligand bound forms

• PDB DOI: 10.2210/pdb4A2L/pdb

• Classification: TRANSCRIPTION
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-09-27 Released: 2012-05-02 
• Deposition Author(s): Lowe, E.C., Basle, A., Czjzek, M., Firbank, S.J., Bolam, D.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.231 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

A Scissor Blade-Like Closing Mechanism Implicated in Transmembrane Signaling in a Bacteroides Hybrid Two-Component System.

Lowe, E.C., Basle, A., Czjzek, M., Firbank, S.J., Bolam, D.N.

(2012) Proc Natl Acad Sci U S A 109: 7298

• PubMed: 22532667 
• DOI: 10.1073/pnas.1200479109
• Primary Citation of Related Structures:  
  4A2L, 4A2M


• PubMed Abstract: 
  

Signaling across the membrane in response to extracellular stimuli is essential for survival of all cells. In bacteria, responses to environmental changes are predominantly mediated by two-component systems, which are typically composed of a membrane-spanning sensor histidine kinase and a cytoplasmic response regulator. In the human gut symbiont Bacteroides thetaiotaomicron, hybrid two-component systems are a key part of the bacterium's ability to sense and degrade complex carbohydrates in the gut. Here, we identify the activating ligand of the hybrid two-component system, BT4663, which controls heparin and heparan sulfate acquisition and degradation in this prominent gut microbe, and report the crystal structure of the extracellular sensor domain in both apo and ligand-bound forms. Current models for signal transduction across the membrane involve either a piston-like or rotational displacement of the transmembrane helices to modulate activity of the linked cytoplasmic kinases. The structures of the BT4663 sensor domain reveal a significant conformational change in the homodimer on ligand binding, which results in a scissor-like closing of the C-termini of each protomer. We propose this movement activates the attached intracellular kinase domains and represents an allosteric mechanism for bacterial transmembrane signaling distinct from previously described models, thus expanding our understanding of signal transduction across the membrane, a fundamental requirement in many important biological processes.

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Organizational Affiliation: 

Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE	A, B, C, D, E, F	795	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_4663
UniProt
Find proteins for Q89YR8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89YR8  Go to UniProtKB:  Q89YR8

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	AA [auth D]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
MES	CA [auth D], GA [auth E], P [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG4	L [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	EA [auth E], G [auth A], H [auth A], HA [auth F], M [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
OAA	FA [auth E], U [auth C], V [auth C]	OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M
PEG	BA [auth D], DA [auth E], IA [auth F], J [auth A], K [auth B], Q [auth C], R [auth C], T [auth C], W [auth D], X [auth D], Y [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	I [auth A], N [auth B], O [auth B], S [auth C], Z [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.231 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 342.468	α = 90
b = 342.468	β = 90
c = 97.852	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
SHELXCDE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-27 
• Released Date: 2012-05-02 
Deposition Author(s): Lowe, E.C., Basle, A., Czjzek, M., Firbank, S.J., Bolam, D.N.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Other
• Version 1.2: 2014-11-19
  Changes: Data collection