Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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: 27.12 kDa 
• Atom Count: 1835 
• Modelled Residue Count: 197 
• Deposited Residue Count: 244 
• Unique protein chains: 1

1R1T

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

• PDB DOI: 10.2210/pdb1R1T/pdb

• Classification: TRANSCRIPTION REPRESSOR
• Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 1.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 

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 
• DOI: 10.1016/j.jmb.2003.09.007
• Primary Citation of Related Structures:  
  1R1T, 1R1U, 1R1V, 1R22, 1R23


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional repressor smtB	A, B	122	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0  Gene Names: smtB, Synpcc7942_1291
UniProt
Find proteins for P30340 (Synechococcus elongatus (strain PCC 7942 / FACHB-805)) Explore P30340  Go to UniProtKB:  P30340

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.24	α = 90
b = 69.722	β = 95.84
c = 43.221	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance