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)

Macromolecule Content

• Total Structure Weight: 50.60 kDa 
• Atom Count: 2802 
• Residue Count: 376 
• Unique protein chains: 1

4PCV

The structure of BdcA (YjgI) from E. coli

• DOI: 10.2210/pdb4PCV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli P0299438.9
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-16 Released: 2015-03-11 
• Deposition Author(s): Page, R., Peti, W., Lord, D.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.222 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Literature

BdcA, a protein important for Escherichia coli biofilm dispersal, is a short-chain dehydrogenase/reductase that binds specifically to NADPH.

Lord, D.M., Baran, A.U., Wood, T.K., Peti, W., Page, R.

(2014) PLoS One 9: e105751-e105751

• PubMed: 25244619 
• DOI: 10.1371/journal.pone.0105751
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The Escherichia coli protein BdcA (previously referred to as YjgI) plays a key role in the dispersal of cells from bacterial biofilms, and its constitutive activation provides an attractive therapeutic target for dismantling these communities. In order to investigate the function of BdcA at a molecular level, we integrated structural and functional studies. Our 2.05 Å structure of BdcA shows that it is a member of the NAD(P)(H)-dependent short-chain dehydrogenase/reductase (SDR) superfamily. Structural comparisons with other members of the SDR family suggested that BdcA binds NADP(H). This was demonstrated experimentally using thermal denaturation studies, which showed that BcdA binds specifically to NADPH. Subsequent ITC experiments further confirmed this result and reported a Kd of 25.9 µM. Thus, BdcA represents the newest member of the limited number of oxidoreductases shown to be involved in quorum sensing and biofilm dispersal.

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Organizational Affiliation: 

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
BdcA (YjgI)	A, B	240	Escherichia coli P0299438.9	Mutation(s): 0  Gene Names: ECP02994389_4551
Find proteins for A0A0J9X1Z4 (Escherichia coli P0299438.9) Go to UniProtKB:  A0A0J9X1Z4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	B	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	A, B	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.222 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.058	α = 90
b = 52.461	β = 118.06
c = 69.807	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-04-16 
• Released Date: 2015-03-11 
Deposition Author(s): Page, R., Peti, W., Lord, D.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB0952550

Revision History 

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence