6J05 | pdb_00006j05

Structures of two ArsR As(III)-responsive repressors: implications for the mechanism of derepression

• PDB DOI: https://doi.org/10.2210/pdb6J05/pdb

• Classification: TRANSCRIPTION
• Organism(s): Acidithiobacillus ferrooxidans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-21 Released: 2019-07-03 
• Deposition Author(s): Prabaharan, C., Kandavelu, P., Packianathan, C., Rosen, P.B., Thiyagarajan, S.
• Funding Organization(s): Other government, National Institutes of Health/National Library of Medicine (NIH/NLM)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Structures of two ArsR As(III)-responsive transcriptional repressors: Implications for the mechanism of derepression.

Prabaharan, C., Kandavelu, P., Packianathan, C., Rosen, B.P., Thiyagarajan, S.

(2019) J Struct Biol 207: 209-217

• PubMed: 31136796 
• DOI: https://doi.org/10.1016/j.jsb.2019.05.009
• Primary Citation Related Structures: 
  6J05, 6J0E


• PubMed Abstract: 
  

  ArsR As(III)-responsive transcriptional repressors, members of the ArsR/SmtB family of metalloregulatory proteins, have been characterized biochemically but, to date, no As(III)-bound structure has been solved. Here we report two crystal structures of ArsR repressors from Acidithiobacillus ferrooxidans (AfArsR) and Corynebacterium glutamicum (CgArsR) in the As(III)-bound form. AfArsR crystallized in P2 ₁ space group and diffracted up to 1.86 Å. CgArsR crystallized in P2 ₁ 2 ₁ 2 ₁ and diffracted up to 1.6 Å. AfArsR showed one As(III) bound in one subunit of the homodimer, while the CgArsR structure showed two As(III) bound with S ₃ coordination, one in each monomer. Previous studies indicated that in AfArsR As(III) binds to Cys95, Cys96 and Cys102 from the same monomer, while, in CgArsR, to Cys15, Cys16 from one monomer and Cys55 from the other monomer. The dimer interfaces of these structures showed distinct differences from other members of the ArsR/SmtB family of proteins, which potentially renders multiple options for evolving metal(loid) binding sites in this family of proteins. Also, CgArsR presents a new α2-N binding site, not the previously predicted α3-N site. Despite differences in the location of the binding cysteines in the primary sequences of these proteins, the two metal binding sites are almost congruent on their structures, an example of convergent evolution. Analyses of the electrostatic surface of the proteins at the DNA binding domain indicate that there two different modes of derepression in the ArsR/SmtB family of metalloregulatory proteins.

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Organizational Affiliation: 
• Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka 560100, India. Electronic address: [e-mail].
SER-CAT, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA. Electronic address: [e-mail].
Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA. Electronic address: [e-mail].
Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA. Electronic address: [e-mail].
Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka 560100, India. Electronic address: [e-mail].

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: 27.89 kDa 
• Atom Count: 1,637 
• Modeled Residue Count: 191 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator ArsR	A, B	124	Acidithiobacillus ferrooxidans	Mutation(s): 0  Gene Names: DN052_10610
UniProt
Find proteins for B7J952 (Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455)) Explore B7J952  Go to UniProtKB:  B7J952

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARS (Subject of Investigation/LOI)	C [auth A]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N
NA	D [auth A], E [auth B], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.922	α = 90
b = 42.727	β = 117.62
c = 49.132	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
AUTOMAR	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Prabaharan, C., Kandavelu, P., Packianathan, C., Rosen, P.B., Thiyagarajan, S.

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Funding Organization	Location	Grant Number
Other government	India	EMR/2014/000299
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	R01 GM55425
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	S10_RR25528
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	S10_RR028976

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2019-08-07
  Changes: Data collection, Database references
• Version 1.2: 2022-03-23
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2023-11-22
  Changes: Data collection, Refinement description