Sandbox Reserved 1063: Difference between revisions

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

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 [[Image:MarR_protein_family_slide.png|500px|left|thumb|'''Figure 1'''. Proteins MarR [http://www.rcsb.org/pdb/explore/explore.do?structureId=3bpx (3BPX)], HucR [http://www.rcsb.org/pdb/explore/explore.do?structureId=2FBK (2FBK)], TcaR [http://www.rcsb.org/pdb/explore/explore.do?structureId=3KP5 (3KP5)], and OhrR [http://www.rcsb.org/pdb/explore/explore.do?structureId=2pfb (2PFB)] are pictured above with conserved features of the MarR protein family highlighted]]
-Contrasting with other members of the MarR family, AdcR is metal dependent. Zinc plays a vital role in organism homeostasis, acting as a [https://en.wikipedia.org/wiki/Cofactor_(biochemistry) 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 <ref> DOI: 10.1021/cr900077w</ref>. The importance of AdcR in ''Streptococcus pneumoniae'' can be understood provided its ability to regulate zinc transfer proteins within the bacteria.
+Contrasting with other members of the MarR family, AdcR is metal dependent. Zinc plays a vital role in organism homeostasis, acting as a [https://en.wikipedia.org/wiki/Cofactor_(biochemistry) 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 <ref> DOI: 10.1021/cr900077w</ref>. Binding of Zinc allows AdcR to bind DNA and activate the transcription of high-affinity Zinc specific uptake transporters. The importance of AdcR in ''Streptococcus pneumoniae'' can be understood provided its ability to regulate zinc transfer proteins within the bacteria.
 ==='''Structural Overview'''===
-One of the two functional domains of AdcR is <scene name='69/694230/Dimerization_domain/3'> dimerization domain</scene>. This domain connects and stabilizes the two pseudosymmetric dimers and is composed of the <scene name='69/694230/Alpha_1/1'>α1 helix</scene>, the C-terminus of the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> , and the <scene name='69/694230/Alpha_6/1'>α6 helix</scene>. This domain is connected to the DNA binding domain by the long α5 helix. The DNA binding domain stabilizes the major and minor groove of DNA via the <scene name='69/694230/Whth_4/7'>winged helix-turn-helix (wHTH)</scene> motif. Binding of Zinc allows AdcR to bind DNA and activate the transcription of high-affinity Zinc specific uptake transporters. The binding of Zinc to the <scene name='69/694230/2_binding_sites/4'>Zinc binding pocket</scene> induces a conformational change that allows for a <scene name='69/694230/Hydrogen_bonding_1/4'>hydrogen bond network</scene> between helices of the binding domain. It is believed that this hydrogen bond network is the allosteric activator needed to expose residues that bind the bases along the major groove of the DNA <ref name="guerra">PMID:22085181</ref>. The binding sites are found adjacent to the DNA binding domain.
+One of the two functional domains of AdcR is <scene name='69/694230/Dimerization_domain/3'> dimerization domain</scene>. This domain connects and stabilizes the two pseudosymmetric dimers and is composed of the <scene name='69/694230/Alpha_1/1'>α1 helix</scene>, the C-terminus of the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> , and the <scene name='69/694230/Alpha_6/1'>α6 helix</scene>. This domain is connected to the DNA binding domain by the long α5 helix. The DNA binding domain stabilizes the major and minor groove of DNA via the <scene name='69/694230/Whth_4/7'>winged helix-turn-helix (wHTH)</scene> motif. The binding of Zinc to the <scene name='69/694230/2_binding_sites/4'>Zinc binding pocket</scene> induces a conformational change that allows for a <scene name='69/694230/Hydrogen_bonding_1/4'>hydrogen bond network</scene> between helices of the binding domain. It is believed that this hydrogen bond network is the allosteric activator needed to expose residues that bind the bases along the major groove of the DNA <ref name="guerra">PMID:22085181</ref>. The binding sites are found adjacent to the DNA binding domain.