7BM2 | pdb_00007bm2

Crystal structure of the DNA-binding protein RemA from Geobacillus thermodenitrificans

• PDB DOI: https://doi.org/10.2210/pdb7BM2/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Geobacillus thermodenitrificans NG80-2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-19 Released: 2021-08-25 
• Deposition Author(s): Altegoer, F., Mrusek, D., Bange, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Structural and functional characterization of the bacterial biofilm activator RemA.

Hoffmann, T., Mrusek, D., Bedrunka, P., Burchert, F., Mais, C.N., Kearns, D.B., Altegoer, F., Bremer, E., Bange, G.

(2021) Nat Commun 12: 5707-5707

• PubMed: 34588455 
• DOI: https://doi.org/10.1038/s41467-021-26005-4
• Primary Citation Related Structures: 
  7BM2, 7BME, 7P1W


• PubMed Abstract: 
  

  Bacillus subtilis can form structurally complex biofilms on solid or liquid surfaces, which requires expression of genes for matrix production. The transcription of these genes is activated by regulatory protein RemA, which binds to poorly conserved, repetitive DNA regions but lacks obvious DNA-binding motifs or domains. Here, we present the structure of the RemA homologue from Geobacillus thermodenitrificans, showing a unique octameric ring with the potential to form a 16-meric superstructure. These results, together with further biochemical and in vivo characterization of B. subtilis RemA, suggests that the protein can wrap DNA around its ring-like structure through a LytTR-related domain.

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Organizational Affiliation: 
• Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany.
Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany.
Department of Biology, Indiana University, Bloomington, IN, USA.
Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany. [e-mail].
Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany. [e-mail].
Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C8  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 39.39 kDa 
• Atom Count: 2,529 
• Modeled Residue Count: 314 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative regulatory protein GTNG_1019	A, B, C, D	87	Geobacillus thermodenitrificans NG80-2	Mutation(s): 0  Gene Names: GTNG_1019
UniProt
Find proteins for A4IM41 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4IM41  Go to UniProtKB:  A4IM41

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B], F [auth B], G [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.91	α = 90
b = 106.91	β = 90
c = 106.91	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-25 
Deposition Author(s): Altegoer, F., Mrusek, D., Bange, G.

Revision History  

• Version 1.0: 2021-08-25
  Type: Initial release
  
• Version 1.1: 2021-10-13
  Changes: Data collection, Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary