Sandbox Reserved 1063

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This Sandbox is Reserved from 02/09/2015, through 05/31/2016 for use in the course "CH462: Biochemistry 2" taught by Geoffrey C. Hoops at the Butler University. This reservation includes Sandbox Reserved 1051 through Sandbox Reserved 1080.

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Contents 1 Zinc-Dependent Transcriptional Regulator AdcR 1.1 Introduction 1.2 Binding Site 1 1.3 Binding Site 2 2 Mechanism of Action 3 Zinc Ligand(s) 4 Other Ligands 5 DNA Binding 5.1 Dimerization Domain 5.2 HTH Domain 6 References

Zinc-Dependent Transcriptional Regulator AdcR

Introduction

AdcR is a zinc-dependent transcriptional regulator that controls the activation of over seventy genes within the bacteria Streptococcus pneumoniae. Zinc plays a vital role in organism homeostasis acting as a [1] and a regulator of enzymatic activity, however zinc can lead to cell toxicity and deficiency of other vital metals that are also necessary for protein function. Given the fundamental role of zinc in general homeostasis the integral role of AdcR in Streptococcus pneumoniae can be seen.

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Zinc-Dependent Transcriptional Regulator AdcR has on each of its two domains (important amino acids for zinc binding shown in white) and can bind a total of four zinc ions at one time. Of the two binding sites, binding site 1 is the only site with known importance for DNA binding. The function of binding site 2 is unknown.

Binding Site 1

consists of a distorted tetrahedral geometry around the zinc ion. The four amino acids involved in zinc binding are E24, H42, H108, and H112.

Binding Site 2

consists of a highly distorted tetrahedral geometry around the zinc ion. There are three amino acids involved in the binding of the zinc ion (C30, E41, and E107) as well as a water molecule. If a C30A mutation is present in binding site 1, it will have no effect on the ability of the protein to bind DNA. Therefore, binding site 2 has no significant role in DNA binding.

Mechanism of Action

Zinc Ligand(s)

Other Ligands

DNA Binding

Dimerization Domain

The dimerization domain is made up of the alpha 1 and C-terminus of the alpha 5 helix.

HTH Domain

The AdcR MarR transcriptional regulator's structure resembles the other proteins in the same family; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif that assists in binding DNA. This wHTH motif is consistent among all marR family proteins that bind DNA. Although AdcR is a highly alpha helical protein, the "wings" of the DNA binding domain consist of two anti parallel beta strands. There is one on each domain of the protein. The winged HTH domain is made up of the alpha 2, alpha 3, alpha 4, beta 1, and beta 2 strands. Alpha 4 is known as the recognition helix that binds the major groove of DNA through hydrogen bonding and Van der Waals interactions between exposed bases. The other helices stabilize the DNA and Protein upon binding.

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References