Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 32.35 kDa 
• Atom Count: 2511 
• Modelled Residue Count: 282 
• Deposited Residue Count: 287 
• Unique protein chains: 1

3QOU

Crystal Structure of E. coli YbbN

• PDB DOI: 10.2210/pdb3QOU/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-10 Released: 2011-02-23 
• Deposition Author(s): Lin, J., Wilson, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Escherichia coli Thioredoxin-like Protein YbbN Contains an Atypical Tetratricopeptide Repeat Motif and Is a Negative Regulator of GroEL.

Lin, J., Wilson, M.A.

(2011) J Biol Chem 286: 19459-19469

• PubMed: 21498507 
• DOI: 10.1074/jbc.M111.238741
• Primary Citation of Related Structures:  
  3QOU


• PubMed Abstract: 
  

Many proteins contain a thioredoxin (Trx)-like domain fused with one or more partner domains that diversify protein function by the modular construction of new molecules. The Escherichia coli protein YbbN is a Trx-like protein that contains a C-terminal domain with low homology to tetratricopeptide repeat motifs. YbbN has been proposed to act as a chaperone or co-chaperone that aids in heat stress response and DNA synthesis. We report the crystal structure of YbbN, which is an elongated molecule with a mobile Trx domain and four atypical tetratricopeptide repeat motifs. The Trx domain lacks a canonical CXXC active site architecture and is not a functional oxidoreductase. A variety of proteins in E. coli interact with YbbN, including multiple ribosomal protein subunits and a strong interaction with GroEL. YbbN acts as a mild inhibitor of GroESL chaperonin function and ATPase activity, suggesting that it is a negative regulator of the GroESL system. Combined with previous observations that YbbN enhances the DnaK-DnaJ-GrpE chaperone system, we propose that YbbN coordinately regulates the activities of these two prokaryotic chaperones, thereby helping to direct client protein traffic initially to DnaK. Therefore, YbbN may play a role in integrating the activities of different chaperone pathways in E. coli and related bacteria.

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Organizational Affiliation: 

Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein ybbN	A	287	Escherichia coli K-12	Mutation(s): 0  Gene Names: ybbN, cnoX, b0492, JW5067
UniProt
Find proteins for P77395 (Escherichia coli (strain K12)) Explore P77395  Go to UniProtKB:  P77395

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.523	α = 90
b = 62.447	β = 96.57
c = 79.981	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-10 
• Released Date: 2011-02-23 
Deposition Author(s): Lin, J., Wilson, M.A.

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2015-05-27
  Changes: Data collection
• Version 1.3: 2017-11-08
  Changes: Refinement description