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== Photosynthesis Response Regulator PrrA of ''Rhodobacter sphaeroides'' ==
= Photosynthesis Response Regulator PrrA of ''Rhodobacter sphaeroides'' =
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== Background Information ==
== Background Information ==
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PrrA is a DNA binding protein and a essential part of the two-component signal transduction regulatory system, PrrBA.  ''Rhodobacter capsulatus'' contains RegA considered a homologue to PrrA protein in ''R. sphaeroides''.  PrrA is proposed to be a master regulator/response regulator involved in oxygen regulation of photosynthesis genes expression responding to changes to the rate of electron flow as means to maintain redox balance, such as a balance between energy production and energy consumption in the cell <ref> Zeilstra-Ryalls, J. H. and S. Kaplan.  2004.  Oxygen Intervention in the Regulation of Gene Expression: The Photosynthetic Bacterial Paradigm.  Cellular and Molecular Life Sciences 61:417-436.</ref>.  PrrA is thought to play an important function in carbon dioxide and nitrogen fixations, photosynthesis as well as proton oxidation and uptake <ref> Eraso, J. M., J. H. Roh, X. Zeng, S. J. Callister, M. S. Lipton and S. Kaplan.  2008. Role of Global Transcriptional Regulator PrrA in ''Rhodobacter sphaeroides'' 2.4.1: Combined Transcriptome and Proteome Analysis.  Journal of Bacteriology 190: 4831-4848.</ref>.   
PrrA of ''Rhodobacter sphaeroides'' is the DNA binding protein partner of the redox-responsive two-component signal transduction regulatory system, PrrBA.  PrrA regulates genes required for carbon dioxide and nitrogen fixations, photosynthesis and proton oxidation and uptake<ref> Eraso, J. M., J. H. Roh, X. Zeng, S. J. Callister, M. S. Lipton and S. Kaplan.  2008. Role of Global Transcriptional Regulator PrrA in ''Rhodobacter sphaeroides'' 2.4.1: Combined Transcriptome and Proteome Analysis.  Journal of Bacteriology 190: 4831-4848.</ref>.   
PrrB is considered a sensor histidine kinase bound to the cytoplasmic membrane that can phosphorylate PrrA when it senses changes the aforementioned changes in the cell.  Interestingly, “1,058 genes were proposed to be regulated out of 4,284 genes as represented on the GeneChip of ''R. sphaeroides'' 2.4.1” by PrrA <ref> Eraso, J. M. and S. Kaplan.  1994.  ''prrA'', a Putative Response Regulator Involved in Oxygen Regulation of Photosynthesis Gene Expression in ''Rhodobacter sphaeroides''.  Journal of Bacteriology 176:32-43.</ref>.
PrrB is an integral membrane sensor histidine kinase that can phosphorylate PrrA when it senses changes in redox, such as can occur when oxygen tension change.  Based on transciptome profiling, of the 4,284 genes represented in ''R. sphaeroides'' 2.4.1 GeneChip, PrrA apparently regulates 1,057<ref> Eraso, J. M. and S. Kaplan.  1994.  ''prrA'', a Putative Response Regulator Involved in Oxygen Regulation of Photosynthesis Gene Expression in ''Rhodobacter sphaeroides''.  Journal of Bacteriology 176:32-43.</ref>.
 
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== Structure of the Proposed PrrA Protein ==
== Structure of the Proposed PrrA Protein ==
<applet load='PrrA.pdb' size='300' color='black' frame='true' align='right' caption='3D Proposed Image of PrrA Protein'/>
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<applet load='PrrA.pdb' size='300' color='black' frame='true' align='right' caption='3D Proposed Image of PrrA Protein'/> http://ca.expasy.org/tools/protparam.html


<scene name='User:Yana_Fedotova/Sandbox_1/Secondary_structure_-_PrrA/1'>Secondary Structure</scene>
*This is the <scene name='User:Yana_Fedotova/Sandbox_1/Prra/4'>Amino to Carboxyl rainbow</scene> of the protein.
{{Template:ColorKey_Amino2CarboxyRainbow}}


<scene name='User:Yana_Fedotova/Sandbox_1/Polar_regions/2'>Polar/Hydrophobic Regions</scene>
*The highlighted <scene name='User:Yana_Fedotova/Sandbox_1/Prra/3'>hydrophobic regions</scene> of the protein.


<scene name='User:Yana_Fedotova/Sandbox_1/N_to_c_rainbow/1'>Amino Terminus to Carboxy Terminus</scene>
*The <scene name='User:Yana_Fedotova/Sandbox_1/Prra/2'>highlighted Glycine and Proline residues</scene> of the protein.


{{Template:ColorKey_Amino2CarboxyRainbow}}


http://ca.expasy.org/tools/protparam.html
The PrrA protein is predicted to consist of a N-terminal receiver domain, extending from 1-130 amino acids, and a C-terminal domain covering approximately from 141-184 amino acids (residues 139-183 are ca. 90% conserved within the protein family<ref> Masuda,S., Matsumoto,Y., Nagashima,K.V., Shimada,K., Inoue,K., Bauer,C.E. and Matsuura,K.  1999.  Structural and Functional Analyses of Photosynthetic Regulatory Genes ''regA'' and ''regB'' from ''Rhodovulum sulfidophilum'', ''Roseobacter denitrificans'' and ''Rhodobacter capsulatus''.  Journal of Bacteriology 181, 4205-4215.</ref>).  It is also suggested that the C-terminal domain contains a helix-turn-helix (HTH) DNA-binding motif from 159-179 amino acids (100% conserved within the family via sequence analysis<ref> Masuda,S., Matsumoto,Y., Nagashima,K.V., Shimada,K., Inoue,K., Bauer,C.E. and Matsuura,K.  1999.  Structural and Functional Analyses of Photosynthetic Regulatory Genes ''regA'' and ''regB'' from ''Rhodovulum sulfidophilum'', ''Roseobacter denitrificans’’ and ''Rhodobacter capsulatus''.  Journal of Bacteriology 181, 4205-4215.</ref>).  The two domains are said to be connected via a short proline-rich linker<ref> Laguri, C., M. K. Phillips-Jones, and M. P. Williamson.  2004. Solution Structure and DNA Binding of the Effector Domain from the Global Regulator PrrA (RegA) from ''Rhodobacter sphaeroides'': Insights into DNA Binding Specificity. Journal of Bacteriology 176:32-43.</ref>.
 
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== Physico-Chemical Properties of PrrA ==
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Molecular weight: 20483.5 Da
Molecular weight: 20483.5 Da
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Theoretical pI: 6.85
Theoretical pI: 6.85
Estimated half-life:
The N-terminal of the sequence considered is M (Met).


The estimated half-life is:  
The estimated half-life is:  
*  30 hours (mammalian reticulocytes, in vitro).
30 hours (mammalian reticulocytes, in vitro).
* >20 hours (yeast, in vivo).
>20 hours (yeast, in vivo).
* >10 hours (Escherichia coli, in vivo).
>10 hours (Escherichia coli, in vivo).


Total number of negatively charged residues (Asp + Glu): 28
Total number of negatively charged residues (Asp + Glu): 28
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Total number of positively charged residues (Arg + Lys): 28
Total number of positively charged residues (Arg + Lys): 28


Atomic composition:
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== Atomic Composition ==
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Carbon      C       894
Carbon      C       894
Hydrogen    H       1468
Hydrogen    H       1468
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Total number of atoms: 2905
Total number of atoms: 2905
Extinction coefficients:


Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water.
Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water.
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Abs 0.1% (=1 g/l)  0.559, assuming NO Cys residues appear as half cystines
Abs 0.1% (=1 g/l)  0.559, assuming NO Cys residues appear as half cystines


Instability index: 55.68
Instability index: 55.68
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Grand Average of Hydropathicity (GRAVY): -0.311
Grand Average of Hydropathicity (GRAVY): -0.311
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== Secondary Structure Composition of PrrA ==
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Alpha-helices: 34.78%
Alpha-helices: 34.78%
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== The Full-Length ''R. sphaeroides'' PrrA Amino Acid Sequence of 184 Residues ==
== The Full-Length '' R. sphaeroides '' PrrA Amino Acid Sequence (184 Residues) ==
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1 maedlvfelg adrslllvdd depflkrlak amekrgfvle taqsvaegka iaqarppaya
1 maedlvfelg adrslllvdd depflkrlak amekrgfvle taqsvaegka iaqarppaya


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| align="center"| 0 || align="center"| 0.0%
| align="center"| 0 || align="center"| 0.0%
|}
|}
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== 1umq ==
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1umq is an engineered chain structure fragment sequence of the DNA binding domain of PrrA with residues from 125 to 184 from ''R. sphaeroides''.  The cited article investigated the C-terminal effector domain of PrrA by NMR, which was said to consist of a three-helix bundle with a helix-turn-helix DNA binding motif.
http://proteopedia.org/wiki/index.php/1umq
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== Phylogenetic Tree of PrrA ==
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http://consurf.tau.ac.il/results/1240259643/treeView.html
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== Evolution of PrrA ==
== Evolution of PrrA ==
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- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.


Phylogenetic Tree of PrrA [http://consurf.tau.ac.il/results/1240259643/treeView.html]


   POS   SEQ     COLOR       RESIDUE VARIETY (Normalized)                        
   POS   SEQ     COLOR       RESIDUE VARIETY (Normalized)                        
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  121   P     4* E,K,N,P
  121   P     4* E,K,N,P


1umq [http://proteopedia.org/wiki/index.php/1umq]


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== Reference ==
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<references/>
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== Animated Image Construction ==
== Animated Image Construction ==
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1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html
1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html
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4. You can edit your protein by using the scene authoring tools after loading the applet.
4. You can edit your protein by using the scene authoring tools after loading the applet.
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== Reference ==
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<references/>
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== Page Creator ==  
== Page Contributor==  
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Yana Fedotova, email: yana.fedotova@gmail.com, yfedot@bgsu.edu
Yana Fedotova, email: yana.fedotova@gmail.com, yfedot@bgsu.edu
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== Acknowledgments ==  
== Acknowledgments ==  
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Dr. Jill Zeilstra-Ryalls, Susana Retamal and Adam Meade
Dr. Jill Zeilstra-Ryalls, Susana Retamal and Adam Meade
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