6XTV | pdb_00006xtv

FULL-LENGTH LTTR LYSG FROM CORYNEBACTERIUM GLUTAMICUM WITH BOUND EFFECTOR ARG

• PDB DOI: https://doi.org/10.2210/pdb6XTV/pdb

• Classification: TRANSCRIPTION
• Organism(s): Corynebacterium glutamicum MB001
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-16 Released: 2020-10-07 
• Deposition Author(s): Hofmann, E., Syberg, F., Schlicker, C., Eggeling, L., Schendzielorz, G.
• Funding Organization(s): German Federal Ministry for Education and Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.251 (Depositor) 
• R-Value Work: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Engineering and application of a biosensor with focused ligand specificity.

Della Corte, D., van Beek, H.L., Syberg, F., Schallmey, M., Tobola, F., Cormann, K.U., Schlicker, C., Baumann, P.T., Krumbach, K., Sokolowsky, S., Morris, C.J., Grunberger, A., Hofmann, E., Schroder, G.F., Marienhagen, J.

(2020) Nat Commun 11: 4851-4851

• PubMed: 32978386 
• DOI: https://doi.org/10.1038/s41467-020-18400-0
• Primary Citation Related Structures: 
  6XTU, 6XTV


• PubMed Abstract: 
  

  Cell factories converting bio-based precursors to chemicals present an attractive avenue to a sustainable economy, yet screening of genetically diverse strain libraries to identify the best-performing whole-cell biocatalysts is a low-throughput endeavor. For this reason, transcriptional biosensors attract attention as they allow the screening of vast libraries when used in combination with fluorescence-activated cell sorting (FACS). However, broad ligand specificity of transcriptional regulators (TRs) often prohibits the development of such ultra-high-throughput screens. Here, we solve the structure of the TR LysG of Corynebacterium glutamicum, which detects all three basic amino acids. Based on this information, we follow a semi-rational engineering approach using a FACS-based screening/counterscreening strategy to generate an L-lysine insensitive LysG-based biosensor. This biosensor can be used to isolate L-histidine-producing strains by FACS, showing that TR engineering towards a more focused ligand spectrum can expand the scope of application of such metabolite sensors.

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Organizational Affiliation: 
• Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, D-52425, Jülich, Germany.
Department of Physics & Astronomy, Brigham Young University, Provo, UT, USA.
Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425, Jülich, Germany.
Protein Crystallography, Biophysics, Ruhr University Bochum, D-44780, Bochum, Germany.
Multiscale Bioengineering, Bielefeld University, D-33615, Bielefeld, Germany.
Department of Physics, Heinrich-Heine University, D-40225, Düsseldorf, Germany.
Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, D-52425, Jülich, Germany.
Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425, Jülich, Germany. [e-mail].
Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074, Aachen, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
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: 63.02 kDa 
• Atom Count: 4,383 
• Modeled Residue Count: 575 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine export transcriptional regulatory protein LysG	A, B	290	Corynebacterium glutamicum MB001	Mutation(s): 0  Gene Names: lysG, Cgl1263, cg1425
UniProt
Find proteins for P94632 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore P94632  Go to UniProtKB:  P94632

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG (Subject of Investigation/LOI)	C [auth B]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.251 (Depositor) 
• R-Value Work:  0.206 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.95	α = 90
b = 123.95	β = 90
c = 111.35	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Hofmann, E., Syberg, F., Schlicker, C., Eggeling, L., Schendzielorz, G.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	FlexFit

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description