Latest revision as of 21:25, 10 May 2009

Photosynthesis Response Regulator PrrA of Rhodobacter sphaeroidesPhotosynthesis Response Regulator PrrA of Rhodobacter sphaeroides

Background InformationBackground Information

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^[1]. 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^[2].

Structure of the Proposed PrrA ProteinStructure of the Proposed PrrA Protein

http://ca.expasy.org/tools/protparam.html

This is the of the protein.

Amino Terminus

Carboxy Terminus

The highlighted of the protein.

The of the protein.

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^[3]). 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^[4]). The two domains are said to be connected via a short proline-rich linker^[5].

Physico-Chemical Properties of PrrAPhysico-Chemical Properties of PrrA

Molecular weight: 20483.5 Da

Number of Amino Acids: 184

Theoretical pI: 6.85

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

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

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

Atomic CompositionAtomic Composition

Carbon C 894 Hydrogen H 1468 Nitrogen N 268 Oxygen O 268 Sulfur S 7

Total number of atoms: 2905

Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.

Ext. coefficient 11585

Abs 0.1% (=1 g/l) 0.566, assuming ALL Cys residues appear as half cystines

Ext. coefficient 11460

Abs 0.1% (=1 g/l) 0.559, assuming NO Cys residues appear as half cystines

Instability index: 55.68

Aliphatic index: 95.49

Grand Average of Hydropathicity (GRAVY): -0.311

Secondary Structure Composition of PrrASecondary Structure Composition of PrrA

Alpha-helices: 34.78%

Extended (Beta-sheets): 20.65%

Other (Loops): 44.57%

The Full-Length R. sphaeroides PrrA Amino Acid Sequence (184 Residues)The Full-Length R. sphaeroides PrrA Amino Acid Sequence (184 Residues)

1 maedlvfelg adrslllvdd depflkrlak amekrgfvle taqsvaegka iaqarppaya

61 vvdlrledgn gldvvevlre rrpdcrivvl tgygaiatav aavkigatdy lskpadanev

121 thallakges lppppenpms adrvrwehiq riyemcdrnv setarrlnmh rrtlqrilak

181 rspr

Amino Acid Composition
Amino Acid	Number present	Percentage of total present
Ala (A)	15	13.0%
Arg (R)	10	10.9%
Asn (N)	6	2.7%
Asp (D)	10	7.1%
Cys (C)	1	1.1%
Gln (Q)	5	2.2%
Glu (E)	11	8.2%
Gly (G)	9	4.9%
His (H)	10	1.6%
Ile (I)	3	3.8%
Leu (L)	21	10.9%
Lys (K)	6	4.3%
Met (M)	6	2.7%
Phe (F)	2	1.6%
Pro (P)	8	6.0%
Ser (S)	7	3.8%
Thr (T)	13	3.8%
Trp (W)	2	0.5%
Tyr (Y)	6	2.2%
Val (V)	12	8.7%
Pyl (O)	0	0.0%
Sec (U)	0	0.0%

1umq1umq

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

Phylogenetic Tree of PrrAPhylogenetic Tree of PrrA

http://consurf.tau.ac.il/results/1240259643/treeView.html

Evolution of PrrAEvolution of PrrA

Amino Acid Conservation Scores

The following scores assist in examining evolutionary relatedness of the amino acid sequence of PrrA to that of other amino acid sequences.

- POS: The position of the AA in the SEQRES derived sequence.

- SEQ: The SEQRES derived sequence in one letter code.

- 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier.

- SCORE: The normalized conservation scores.

- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).

- CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores.

- CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval.

- MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position.

- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.

 POS	  SEQ	    		COLOR		      RESIDUE VARIETY (Normalized)	        	               
  1	   D	    		  7		    	D,N,R             
  2	   R	    		  4		    	K,P,Q,R,Y         
  3	   S	    	 	  7			K,N,S,T           
  4	   L	    		  7			A,I,L,V           
  5	   L	    		  8			A,F,H,L           
  6	   L	    		  5			I,L,V             
  7	   V	    		  8			A,I,L,V           
  8	   D	    		  9			D,E               
  9	   D	    		  9			D                 
 10	   D	    		  7			D,E,N             
 11	   E	    		  1			A,D,E,I,K,N,P,Q,R,S,T,V
 12	   P	    	 	  3			A,D,E,G,K,L,N,P,S 
 13	   F	    	 	  7			F,H,I,L,T,V       
 14	   L	    		  6			A,C,G,L,R,S,V     
 15	   K	    		  1			D,E,G,H,K,N,Q,R,T,W
 16	   R	    		  2			A,F,G,I,L,M,R,S,T,V,W,Y
 17	   L	    		  7			F,I,L,M,T,V       
 18	   A	    		  2		    	A,E,G,I,N,Q,R,S,T 
 19	   K	    		  1			A,F,G,I,K,L,Q,R,T,V,Y
 20	   A	    		  6	    		A,C,G,I,L,M,N,R,S,T
 21	   M	    		  8			A,F,I,L,M         
 22	   E	    		  4			A,E,G,K,Q,R,S,T,V 
 23	   K	    		  1			A,D,E,F,G,K,L,M,Q,R,S,T
 24	   R	    		  3			A,D,E,L,M,N,Q,R,S,W
 25	   G	    		  9			G,K               
 26	   F	    		  4			F,H,L,M,Y         
 27	   V	    		  1			A,D,E,K,L,N,Q,R,S,T,V
 28	   L	    		  7			A,C,L,P,T,V       
 29	   E	    		  2			A,D,E,F,H,I,K,L,R,S,T,V,Y
 30	   T	    		  1			A,C,E,H,I,L,M,Q,S,T,V,W
 31	   A	    		  7			A,F,H,T,V,Y       
 32	   Q	    		  1			A,D,E,F,G,H,N,Q,R,S,T,Y
 33	   S	    		  6			D,G,H,L,N,S,T     
 34	   V	    		  6			A,G,L,S,T,V       
 35	   A	    		  1			A,D,E,H,K,L,N,P,Q,R,S,T,V
 36	   E	    		  1			A,D,E,G,M,N,Q,R,S,T
 37	   G	    		  7			A,F,G,L,V         
 38	   K	    		  2			D,E,H,I,K,L,M,R,V,W,Y
 39	   A	    		  1			A,D,E,H,K,L,Q,R,T 
 40	   I	    		  1			A,D,E,F,G,I,K,L,M,Q,S,V,W
 41	   A	    		  1			A,F,G,I,L,M,V     
 42	   Q	    		  1		   	A,E,H,I,K,L,M,N,P,Q,R,S,T,V
 43	   A	    		  2			A,D,E,I,N,P,R,S,T 
 44	   R	    		  1			A,D,E,G,I,K,L,N,Q,R,V,Y
 45	   P	    		  1			A,D,E,F,H,I,K,M,P,Q,R,T,V
 46	   P	    		  4			A,F,G,N,P,R,V,Y   
 47	   A	    		  7			A,D,G,H,K,N,Q,S   
 48	   Y	    		  5			A,C,H,I,L,P,V,Y   
 49	   A	    		  5			A,C,I,L,V         
 50	   V	    		  4			F,I,L,V           
 51	   V	    		  6			C,F,I,L,M,S,T,V   
 52	   D	    		  9			D                 
 53	   L	    		  6			I,L,M,V,W         
 54	   R	    		  7			G,K,M,N,R,T,V,W   
 55	   L	    		  7			L,M               
 56	   E	    		  7			A,D,E,G,P,S       
 57	   D	    		  4			D,E,G,K,N,R       
 58	   G	    		  5			D,E,G,I,K,L,M,T,V 
 59	   N	    		  7			D,N,S,T           
 60	   G	    		  9			A,G               
 61	   L	    		  6			F,I,L,M,V,W       
 62	   D	    		  5			A,D,E,G,H,K,Q,S   
 63	   V	    		  6			A,F,I,L,T,V       
 64	   V	    		  4			A,C,F,I,L,V       
 65	   E	    		  4			A,D,E,H,K,P,Q,R,Y 
 66	   V	    		  1			A,D,E,I,K,M,N,Q,R,T,V,Y
 67	   L	    		  7			I,L,M,V,W         
 68	   R	    		  7			G,K,L,N,Q,R       
 69	   E	    		  1			A,D,E,G,I,K,Q,R,S,V
 70	   R	    		  1		   	A,D,E,H,I,K,L,M,N,Q,R,S,T,V,W
 71	   R	    		  1			A,D,E,G,H,K,N,Q,R,S,Y
 72	   P	    		  5			A,D,I,K,L,P,Q,T,V,Y
 73	   D	    		  3			A,D,E,G,H,L,M,N,Q,R,T,W
 74	   C	    		  3			A,C,F,I,L,M,T,V   
 75	   R	    		  8			A,K,P,R           
 76	   I	    		  7			I,M,S,V           
 77	   V	    		  7			A,I,L,M,V         
 78	   V	    		  6			F,I,L,M,V         
 79	   L	    		  7			I,L,M,V           
 80	   T	    		  9			S,T               
 81	   G	    		  9			A,G,S             
 82	   Y	    		  7			F,H,K,L,Q,R,S,Y   
 83	   G	    		  6			A,D,G,N,S         
 84	   A	    		  5			A,D,E,N,S,T       
 85	   I	    		  6			E,F,I,L,V         
 86	   A	    		  4			A,D,E,F,I,M,P,S,T 
 87	   T	    		  8			A,D,E,H,L,M,N,T   
 88	   A	    		  9			A,E,K,R           
 89	   V	   		  8			I,L,V             
 90	   A	   		  2			A,D,E,F,I,K,L,N,Q,S
 91	   A	   		  9			A,G,T             
 92	   V	   		  6			A,F,I,L,M,S,T,V,Y 
 93	   K	   		  5			A,D,E,K,N,Q,R     
 94	   I	   		  1		   	A,C,D,G,H,I,K,L,M,Q,R,S,T,V
 95	   G	   		  9			G                 
 96	   A	   		  9			A,S,V             
 97	   T	   		  5			A,D,F,L,Q,T,V,Y   
 98	   D	   		  9			D,E,S             
 99	   Y	   		  7			F,Y               
100	   L	   		  7			I,L,M,V           
101	   S	   		  6			A,C,E,I,P,S,T,V   
102	   K	   		  9			K                 
103	   P	   		  9			P                 
104	   A	   		  7			A,C,F,L,V         
105	   D	   		  7			A,D,E,G,H,N,S     
106	   A	   		  4			A,D,F,I,K,L,N,P,T 
107	   N	   		  6			A,D,E,G,K,N,R,T   
108	   E	   		  5			A,D,E,K,N,Q,R,V   
109	   V	   		  6			I,L,M,T,V         
110	   T	   		  1			A,D,I,L,N,Q,R,T,V,Y
111	   H	   		  7			A,E,H,L,N,Q       
112	   A	   		  8			A,L,R,S,T         
113	   L	   		  5			I,L,V             
114	   L	   		  4			E,H,I,K,L,Q,R     
115	   A	   		  6			A,Q,R,S,T         
116	   K	   		  4			A,I,K,L,N,R,V     
117	   G	   		  6			G,L,S,V           
118	   E	   		  8			E,R               
119	   S	   		  6			A,H,R,S           
120	   L	   		  6			G,L,S             
121	   P	   		  4*			E,K,N,P

Animated Image ConstructionAnimated Image Construction

1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html

2. On the submission form, first select 'animation' in the "type of request" section, select the size of the animation to be generated in pixels(here the size is 600), then upload the PDB format protein structure file in the "source of structural data" section.

3. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'.

4. On "advanced structural annotation" section select 'docking models in Capri format'.

5. Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated.

JMol Image ConstructionJMol Image Construction

1. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.

2. Go to 3D-JIGSAW page http://bmm.cancerresearchuk.org/~3djigsaw/ and paste the sequence on the submission page. A .pdb format image of your protein will be sent to you on your email which can be opened by RASMOL.

3. Upload this file on Proteopedia and then load the JMol applet for the protein following instructions on the Help:Editing page http://www.proteopedia.org/wiki/index.php/Help:Editing.

4. You can edit your protein by using the scene authoring tools after loading the applet.

ReferenceReference

↑ 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.
↑ 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.
↑ 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.
↑ 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.
↑ 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.

Page ContributorPage Contributor

Yana Fedotova, email: yana.fedotova@gmail.com, yfedot@bgsu.edu

AcknowledgmentsAcknowledgments

Dr. Jill Zeilstra-Ryalls, Susana Retamal and Adam Meade

[1] 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.

[2] 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.

[3] 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.

[4] 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.

[5] 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.

[1]

[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
 ''
-== Photosynthesis Response Regulator PrrA of ''Rhodobacter sphaeroides'' ==
+= Photosynthesis Response Regulator PrrA of ''Rhodobacter sphaeroides'' =
 ''
 ''
 == Background Information ==
 ''
-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>.
 ''
 == 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'/>
+''
+<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
+*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/Secondary_structure_-_PrrA/1'>Secondary Structure</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/Polar_regions/2'>Polar/Hydrophobic Regions</scene>
+*The <scene name='User:Yana_Fedotova/Sandbox_1/Prra/2'>highlighted Glycine and Proline residues</scene> of the protein.
-<scene name='User:Yana_Fedotova/Sandbox_1/N_to_c_rainbow/1'>Amino Terminus to Carboxy Terminus</scene>
-{{Template:ColorKey_Amino2CarboxyRainbow}}
+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>.
-http://ca.expasy.org/tools/protparam.html
+''
+== Physico-Chemical Properties of PrrA ==
+''
 Molecular weight: 20483.5 Da
@@ Line 26: / Line 33: @@
 Theoretical pI: 6.85
-Estimated half-life:
-The N-terminal of the sequence considered is M (Met).
 The estimated half-life is:
-*  30 hours (mammalian reticulocytes, in vitro).
+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
@@ Line 40: / Line 43: @@
 Total number of positively charged residues (Arg + Lys): 28
-Atomic composition:
+''
+== Atomic Composition ==
+''
 Carbon      C	       894
 Hydrogen    H	      1468
@@ Line 48: / Line 54: @@
 Total number of atoms: 2905
-Extinction coefficients:
 Extinction coefficients are in units of  M-1 cm-1, at 280 nm measured in water.
@@ Line 60: / Line 64: @@
 Abs 0.1% (=1 g/l)   0.559, assuming NO Cys residues appear as half cystines
 Instability index: 55.68
@@ Line 67: / Line 70: @@
 Grand Average of Hydropathicity (GRAVY): -0.311
+''
+== Secondary Structure Composition of PrrA ==
+''
 Alpha-helices: 34.78%
@@ Line 75: / Line 82: @@
 ''
-== The Full-Length ''R. sphaeroides'' PrrA Amino Acid Sequence of 184 Residues ==
+== The Full-Length '' R. sphaeroides '' PrrA Amino Acid Sequence (184 Residues) ==
 ''
 maedlvfelg adrslllvdd depflkrlak amekrgfvle taqsvaegka iaqarppaya
@@ Line 156: / Line 164: @@
 | align="center"| 0 || align="center"| 0.0%
 |}
+''
+== 1umq ==
+''
+umq 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
+''
+== Phylogenetic Tree of PrrA ==
+''
+http://consurf.tau.ac.il/results/1240259643/treeView.html
 ''
 == Evolution of PrrA ==
@@ Line 183: / Line 207: @@
 - 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)
@@ Line 307: / Line 330: @@
 	   L	   		  6			G,L,S
 	   P	   		  4*			E,K,N,P
-umq [http://proteopedia.org/wiki/index.php/1umq]
 ''
-== Reference ==
+== Animated Image Construction ==
 ''
-<references/>
-ANIMATED IMAGE CONSTRUCTION:
 . Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html
@@ Line 329: / Line 346: @@
 . Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated.
+''
-JMOL IMAGE CONSTRUCTION:
+== JMol Image Construction ==
+''
 . First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.
@@ Line 339: / Line 357: @@
 . You can edit your protein by using the scene authoring tools after loading the applet.
+''
+== Reference ==
+''
+<references/>
 ''
-== Page Creator ==
+== Page Contributor==
 ''
 Yana Fedotova, email: yana.fedotova@gmail.com, yfedot@bgsu.edu
 ''
 == Acknowledgments ==
 ''
 Dr. Jill Zeilstra-Ryalls, Susana Retamal and Adam Meade

User:Yana Fedotova/Sandbox 1: Difference between revisions

Latest revision as of 21:25, 10 May 2009

Contents

Photosynthesis Response Regulator PrrA of Rhodobacter sphaeroidesPhotosynthesis Response Regulator PrrA of Rhodobacter sphaeroides

Background InformationBackground Information

Structure of the Proposed PrrA ProteinStructure of the Proposed PrrA Protein

Physico-Chemical Properties of PrrAPhysico-Chemical Properties of PrrA

Atomic CompositionAtomic Composition

Secondary Structure Composition of PrrASecondary Structure Composition of PrrA

The Full-Length R. sphaeroides PrrA Amino Acid Sequence (184 Residues)The Full-Length R. sphaeroides PrrA Amino Acid Sequence (184 Residues)

1umq1umq

Phylogenetic Tree of PrrAPhylogenetic Tree of PrrA

Evolution of PrrAEvolution of PrrA

Animated Image ConstructionAnimated Image Construction

JMol Image ConstructionJMol Image Construction

ReferenceReference

Page ContributorPage Contributor

AcknowledgmentsAcknowledgments

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User:Yana Fedotova/Sandbox 1: Difference between revisions

Latest revision as of 21:25, 10 May 2009

Photosynthesis Response Regulator PrrA of Rhodobacter sphaeroidesPhotosynthesis Response Regulator PrrA of Rhodobacter sphaeroides

Background InformationBackground Information

Structure of the Proposed PrrA ProteinStructure of the Proposed PrrA Protein

Physico-Chemical Properties of PrrAPhysico-Chemical Properties of PrrA

Atomic CompositionAtomic Composition

Secondary Structure Composition of PrrASecondary Structure Composition of PrrA

The Full-Length R. sphaeroides PrrA Amino Acid Sequence (184 Residues)The Full-Length R. sphaeroides PrrA Amino Acid Sequence (184 Residues)

1umq1umq

Phylogenetic Tree of PrrAPhylogenetic Tree of PrrA

Evolution of PrrAEvolution of PrrA

Animated Image ConstructionAnimated Image Construction

JMol Image ConstructionJMol Image Construction

ReferenceReference

Page ContributorPage Contributor

AcknowledgmentsAcknowledgments

Navigation menu

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