Sandbox Reserved 1063

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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Zinc-Dependent Transcriptional Regulator AdcRZinc-Dependent Transcriptional Regulator AdcR

IntroductionIntroduction

AdcR is a zinc-dependent transcriptional regulator that controls the activation of over seventy genes within the bacteria Streptococcus pneumoniae^[1]. Zinc plays a vital role in organism homeostasis acting as a co-factor 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^[2]^[3]. Given the fundamental role of zinc in general homeostasis the integral role of AdcR in Streptococcus pneumoniae can be seen given its ability to regulate zinc transfer proteins within the bacteria. Consistent with AdcR's identity as a member of the MarR protein family, AdcR exhibits a triangular shape consisting of a two fold pseudosymetric homo dimer with its own unique winged helix-turn-helix (wHTH) binding domain. This structure calls for multiple zinc binding sites that facilitate protein conformational change allowing for DNA binding and regulation through the wHTH domain.

Figure Legend

Write general information about protein here

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 1Binding 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 2Binding 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 ActionMechanism of Action

Zinc Ligand(s)Zinc Ligand(s)

Other LigandsOther Ligands

DNA BindingDNA Binding

Zinc's Allosteric ActivationZinc's Allosteric Activation

The binding of Zinc allows for the conformational change that induces the binding of DNA in order to activate genes. The binding of Zinc metals creates a hydrogen bond network within the protein that connects the metal binding sites and the DNA binding domain. Most importantly, the hydrogen bonding network connects the metal binding pockets to the alpha 4 helix, which is known as the recognition helix. Alpha 4 helix plays a crucial role in binding DNA. The hydrogen bond network acts as an allosteric activator for the protein to bind DNA. The hydrogen bond network connects the alpha 2 and alpha 4 helix via hydrogen bonding between specific residues. After zinc is bound, a E24 residue from a random coil accepts a hydrogen bond from the carboxamide end of a N38 residue from the alpha 2 helix. Then, a Q40 residue from alpha 2 helix accepts a hydrogen bond from a S74 residue from the alpha 4 helix. The same is seen across the MarR family as a whole. Now the protein is ready to bind DNA.

Helix-Turn-Helix DomainHelix-Turn-Helix 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 HTH domain is made up of the alpha 2, alpha 3, alpha 4 helices. The recognition helix, or the alpha 4 helix, binds the major groove of DNA through hydrogen bonding and Van der Waals interactions between exposed bases. The wings of the helix bind the minor groove of DNA while the other helices stabilize the DNA and Protein upon binding. The two anti parallel beta sheets contain several Arginine residues and other positive amino acids that stabilize this interaction between DNA.

</StructureSection>

ReferencesReferences

↑ Sanson M, Makthal N, Flores AR, Olsen RJ, Musser JM, Kumaraswami M. Adhesin competence repressor (AdcR) from Streptococcus pyogenes controls adaptive responses to zinc limitation and contributes to virulence. Nucleic Acids Res. 2015 Jan;43(1):418-32. doi: 10.1093/nar/gku1304. Epub 2014 Dec, 15. PMID:25510500 doi:http://dx.doi.org/10.1093/nar/gku1304
↑ Fraústo da Silva J, Williams R. The Biological Chemistry of Elements: The Inorganic Chemistry of Life. Second ed. Oxford University Press; Oxford: 2001.
↑ Ma Z, Jacobsen FE, Giedroc DP. Coordination chemistry of bacterial metal transport and sensing. Chem Rev. 2009 Oct;109(10):4644-81. doi: 10.1021/cr900077w. PMID:19788177 doi:http://dx.doi.org/10.1021/cr900077w

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA, Zach LaRoche, Paxton Schowe, Geoffrey C. Hoops, Alexi Zaniker, Shandeep Singh, Isaac C. Gluesenkamp

[1] Sanson M, Makthal N, Flores AR, Olsen RJ, Musser JM, Kumaraswami M. Adhesin competence repressor (AdcR) from Streptococcus pyogenes controls adaptive responses to zinc limitation and contributes to virulence. Nucleic Acids Res. 2015 Jan;43(1):418-32. doi: 10.1093/nar/gku1304. Epub 2014 Dec, 15. PMID:25510500 doi:http://dx.doi.org/10.1093/nar/gku1304

[2] Fraústo da Silva J, Williams R. The Biological Chemistry of Elements: The Inorganic Chemistry of Life. Second ed. Oxford University Press; Oxford: 2001.

[3] Ma Z, Jacobsen FE, Giedroc DP. Coordination chemistry of bacterial metal transport and sensing. Chem Rev. 2009 Oct;109(10):4644-81. doi: 10.1021/cr900077w. PMID:19788177 doi:http://dx.doi.org/10.1021/cr900077w

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