Biological Assembly 1  

 3D View: Structure | Electron Density | 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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.92 kDa 
• Atom Count: 2206 
• Residue Count: 269 
• Unique protein chains: 1

5XP0

Crystal structure of master biofilm regulator CsgD regulatory domain

• DOI: 10.2210/pdb5XP0/pdb

• Classification: TRANSCRIPTION
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-31 Released: 2018-06-20 
• Deposition Author(s): Wen, Y., Ouyang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Literature

Crystal structure of master biofilm regulator CsgD regulatory domain reveals an atypical receiver domain.

Wen, Y., Ouyang, Z., Devreese, B., He, W., Shao, Y., Lu, W., Zheng, F.

(2017) Protein Sci 26: 2073-2082

• PubMed: 28758290 
• DOI: 10.1002/pro.3245
• Primary Citation of Related Structures:  
  5XP0


• PubMed Abstract: 
  

The master regulator CsgD switches planktonic growth to biofilm formation by activating synthesis of curli fimbriae and cellulose in Enterobacteriaceae. CsgD was classified to be the LuxR response regulatory family, while its cognate sensor histidine kinase has not been identified yet. CsgD consists of a C-terminal DNA binding domain and an N-terminal regulatory domain that provokes the upstream signal transduction to further modulate its function. We provide the crystal structure of Salmonella Typhimurium CsgD regulatory domain, which reveals an atypical β5α5 response regulatory receiver domain folding with the α2 helix representing as a disorder loop compared to the LuxR/FixJ canonical response regulator, and the structure indicated a noteworthy α5 helix similar to the non-canonical master regulator VpsT receiver domain α6. CsgD regulatory domain assembles with two dimerization interfaces mainly through α1 and α5, which has shown similarity to the c-di-GMP independent and stabilized dimerization interface of VpsT from Vibrio cholerae respectively. The potential phosphorylation site D59 is directly involved in the interaction of interfaces I and mutagenesis studies indicated that both dimerization interfaces could be crucial for CsgD activity. The structure reveals important molecular details for the dimerization assembly of CsgD and will shed new insight into its regulation mechanism.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable csgAB operon transcriptional regulatory protein	A, B	155	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: csgD, STM1142
Find proteins for O54294 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore O54294  Go to UniProtKB:  O54294

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.758	α = 90
b = 57.758	β = 90
c = 207.742	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-05-31 
• Released Date: 2018-06-20 
Deposition Author(s): Wen, Y., Ouyang, Z.

Revision History 

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2019-07-03
  Changes: Data collection, Database references, Structure summary