User:Yana Fedotova/Sandbox 1: Difference between revisions
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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 | 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>. | ||
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 | 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>. | ||
'' | '' | ||
== 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'/> | |||
<scene name='User:Yana_Fedotova/Sandbox_1/Secondary_structure_-_PrrA/1'>Secondary Structure</scene> | |||
<scene name='User:Yana_Fedotova/Sandbox_1/Polar_regions/2'>Polar/Hydrophobic Regions</scene> | |||
<scene name='User:Yana_Fedotova/Sandbox_1/N_to_c_rainbow/1'>Amino Terminus to Carboxy Terminus</scene> | |||
{{Template:ColorKey_Amino2CarboxyRainbow}} | |||
http://ca.expasy.org/tools/protparam.html | http://ca.expasy.org/tools/protparam.html | ||
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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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ANIMATED IMAGE | ANIMATED IMAGE CONSTRUCTION: | ||
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. | ||
'' | '' | ||
== Page | == Page Creator == | ||
'' | '' | ||
Yana Fedotova, email: yana.fedotova@gmail.com, yfedot@bgsu.edu | Yana Fedotova, email: yana.fedotova@gmail.com, yfedot@bgsu.edu | ||
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'' | '' | ||
Dr. Jill Zeilstra-Ryalls, Susana Retamal and Adam Meade | Dr. Jill Zeilstra-Ryalls, Susana Retamal and Adam Meade | ||
Revision as of 17:40, 1 May 2009
Photosynthesis Response Regulator PrrA of Rhodobacter sphaeroidesPhotosynthesis Response Regulator PrrA of Rhodobacter sphaeroides
Background InformationBackground 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 [1]. PrrA is thought to play an important function in carbon dioxide and nitrogen fixations, photosynthesis as well as proton oxidation and uptake [2]. 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 [3].
Structure of the Proposed PrrA ProteinStructure of the Proposed PrrA Protein
|
| Amino Terminus | Carboxy Terminus |
http://ca.expasy.org/tools/protparam.html
Molecular weight: 20483.5 Da
Number of Amino Acids: 184
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).
- >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 composition: Carbon C 894 Hydrogen H 1468 Nitrogen N 268 Oxygen O 268 Sulfur S 7
Total number of atoms: 2905
Extinction coefficients:
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
Alpha-helices: 34.78%
Extended (Beta-sheets): 20.65%
Other (Loops): 44.57%
The Full-Length R. sphaeroides PrrA Amino Acid Sequence of 184 ResiduesThe Full-Length R. sphaeroides PrrA Amino Acid Sequence of 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 | 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% |
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.
Phylogenetic Tree of PrrA [1]
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
1umq [2]
ReferenceReference
- ↑ 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.
- ↑ 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.
ANIMATED 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 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.
Page CreatorPage Creator
Yana Fedotova, email: yana.fedotova@gmail.com, yfedot@bgsu.edu
AcknowledgmentsAcknowledgments
Dr. Jill Zeilstra-Ryalls, Susana Retamal and Adam Meade