8SVA | pdb_00008sva

Structure of the Rhodococcus sp. USK13 DarR-20 bp DNA complex

• PDB DOI: https://doi.org/10.2210/pdb8SVA/pdb
• NAKB: 8SVA

• Classification: TRANSCRIPTION/DNA
• Organism(s): Rhodococcus sp. USK13, Rhodococcus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-15 Released: 2023-11-01 
• Deposition Author(s): Schumacher, M.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 
  0.276 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Literature

Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding.

Schumacher, M.A., Lent, N., Chen, V.B., Salinas, R.

(2023) Nat Commun 14: 7239-7239

• PubMed: 37945601 
• DOI: https://doi.org/10.1038/s41467-023-42823-0
• Primary Citation Related Structures: 
  8SUA, 8SUK, 8SV6, 8SVA, 8SVD, 8T5Y


• PubMed Abstract: 
  

  The mycobacterial repressor, DarR, a TetR family regulator (TFR), was the first transcription regulator shown to bind c-di-AMP. However, the molecular basis for this interaction and the mechanism involved in DNA binding by DarR remain unknown. Here we describe DarR-c-di-AMP and DarR-DNA structures and complementary biochemical assays. The DarR-c-di-AMP structure reveals a unique effector binding site for a TFR, located between DarR dimer subunits. Strikingly, we show this motif also binds cAMP. The location of the adenine nucleotide binding site between subunits suggests this interaction may facilitate dimerization and hence DNA binding. Indeed, biochemical assays show cAMP enhances DarR DNA binding. Finally, DarR-DNA structures reveal a distinct TFR DNA-binding mechanism involving two interacting dimers on the DNA. Thus, the combined data unveil a newly described second messenger binding motif and DNA binding mode for this important family of regulators.

---

Organizational Affiliation: 
• Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA. [e-mail].
Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 107.35 kDa 
• Atom Count: 6,833 
• Modeled Residue Count: 827 
• Deposited Residue Count: 888 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR/AcrR family transcriptional regulator	A, B [auth F], C [auth G], D [auth T]	212	Rhodococcus sp. USK13	Mutation(s): 0  Gene Names: C5613_22450
UniProt
Find proteins for A0A2S8J6Y8 (Rhodococcus opacus) Explore A0A2S8J6Y8  Go to UniProtKB:  A0A2S8J6Y8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*AP*TP*AP*CP*TP*CP*CP*GP*GP*AP*GP*TP*AP*TP*CP*TP*A)-3')	E [auth B], F [auth D]	20	Rhodococcus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free:  0.276 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.894	α = 90
b = 128.894	β = 90
c = 113.929	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data reduction
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Schumacher, M.A.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM130290

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release
  
• Version 1.1: 2023-11-15
  Changes: Data collection
• Version 1.2: 2023-11-22
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Source and taxonomy
• Version 1.4: 2024-10-16
  Changes: Structure summary