5YSZ | pdb_00005ysz

transcriptional regulator CelR-cellobiose complex

• PDB DOI: https://doi.org/10.2210/pdb5YSZ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Thermobifida fusca YX
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-16 Released: 2018-08-22 
• Deposition Author(s): Fu, Y., Yeom, S.Y., Lee, D.H., Lee, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.167 (Depositor), 0.154 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Structural and functional analyses of the cellulase transcription regulator CelR

Fu, Y., Yeom, S.J., Kwon, K.K., Hwang, J., Kim, H., Woo, E.J., Lee, D.H., Lee, S.G.

(2018) FEBS Lett 592: 2776-2785

• PubMed: 30062758 
• DOI: https://doi.org/10.1002/1873-3468.13206
• Primary Citation Related Structures: 
  5YSZ


• PubMed Abstract: 
  

  CelR is a transcriptional regulator that controls the expression of cellulases catalyzing cellulose hydrolysis. However, the structural mechanism of its regulation has remained unclear. Here, we report the first structure of CelR, in this case with cellobiose bound. CelR consists of a DNA-binding domain (DBD) and a regulatory domain (RD), and homodimerizes with each monomer bound to cellobiose. A hinge region (HR) in CelR connects the DBD with the RD, and Leu59 in the HR acts as a 'leucine lever' that transduces a transcriptional activation signal. Furthermore, an α4 helix mediates the ligand-binding signal for transcriptional activation. Tyr84 and Gln301 can potentially alter the ligand specificity of CelR. This study provides a pivotal step toward understanding transcription of the cellulases.

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Organizational Affiliation: 
• Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.
The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, China.
Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.
Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Korea.
Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.
Department of Bio-Analytical Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
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: 39.51 kDa 
• Atom Count: 2,910 
• Modeled Residue Count: 327 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family	A	360	Thermobifida fusca YX	Mutation(s): 0  Gene Names: Tfu_0938
UniProt
Find proteins for Q47RE1 (Thermobifida fusca (strain YX)) Explore Q47RE1  Go to UniProtKB:  Q47RE1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	B	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.167 (Depositor), 0.154 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.577	α = 90
b = 122.428	β = 121.46
c = 47.498	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
Coot	model building
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Fu, Y., Yeom, S.Y., Lee, D.H., Lee, S.G.

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Funding Organization	Location	Grant Number
	Korea, Republic Of	--

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary