Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 27122.95 
• Atom Count: 1556 
• Residue Count: 244 
• Unique protein chains: 1

1R1T

Crystal structure of the cyanobacterial metallothionein repressor SmtB in the apo-form

• DOI: 10.2210/pdb1R1T/pdb

• Classification: TRANSCRIPTION REPRESSOR
• Organism(s): Synechococcus elongatus (strain PCC 7942)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2003-09-25 Released: 2004-05-18 
• Deposition Author(s): Eicken, C., Pennella, M.A., Chen, X., Koshlap, K.M., VanZile, M.L., Sacchettini, J.C., Giedroc, D.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.249 
• R-Value Work: 0.216 

Literature

A metal-ligand-mediated intersubunit allosteric switch in related SmtB/ArsR zinc sensor proteins.

Eicken, C., Pennella, M.A., Chen, X., Koshlap, K.M., VanZile, M.L., Sacchettini, J.C., Giedroc, D.P.

(2003) J.Mol.Biol. 333: 683-695

• PubMed: 14568530 
• Primary Citation of Related Structures:  
  1R23, 1R22, 1R1V, 1R1U


• PubMed Abstract: 
  

The origin of metal ion selectivity by members of the SmtB/ArsR family of bacterial metal-sensing transcriptional repressors and the mechanism of negative allosteric regulation of DNA binding is poorly understood. Here, we report that two homologous zinc sensors, Staphylococcus aureus CzrA and cyanobacterial SmtB, are "winged" helix homodimeric DNA-binding proteins that bind Zn(II) to a pair of tetrahedral, interhelical binding sites, with two ligands derived from the alpha5 helix of one subunit, Asp84 O(delta1) (Asp104 in SmtB), His86 N(delta1) (His106), and two derived from the alpha5 helix of the other, His97' N(delta1) (His117') and His100' N(epsilon2) (Glu120'). Formation of the metal chelate drives a quaternary structural switch mediated by an intersubunit hydrogen-binding network that originates with the non-liganding N(epsilon2) face of His97 in CzrA (His117 in SmtB) that stabilizes a low-affinity, DNA-binding conformation. The structure of the Zn(1) SmtB homodimer shows that both metal-binding sites of the dimer must be occupied for the quaternary structural switch to occur. Thus, a critical zinc-ligating histidine residue obligatorily couples formation of the metal-sensing coordination chelate to changes in the conformation and dynamics of the putative DNA-binding helices.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Center for Structural Biology, Texas A&M University, College Station, TX 77843-2128, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Transcriptional repressor smtB	A, B	122	Synechococcus elongatus (strain PCC 7942)	Mutation(s): 0  Gene Names: smtB
Find proteins for P30340 (Synechococcus elongatus (strain PCC 7942)) Go to UniProtKB:  P30340

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.249 
• R-Value Work: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 37.240	α = 90.00
b = 69.722	β = 95.84
c = 43.221	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
CNS	phasing
SCALEPACK	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-25 
• Released Date: 2004-05-18 
• Deposition Author(s): Eicken, C., Pennella, M.A., Chen, X., Koshlap, K.M., VanZile, M.L., Sacchettini, J.C., Giedroc, D.P.

Revision History 

• Version 1.0: 2004-05-18
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance