Coding

Part:BBa_K1150004

Designed by: Freiburg 2013   Group: iGEM13_Freiburg   (2013-09-16)
Revision as of 00:38, 9 October 2013 by TU Munich (Talk | contribs) (→‎Sequence and Features)

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PhyB

PhyB
Function Photoreceptor
Use in Mammalian cells
RFC standard RFC 25
Backbone pSB1C3
Organism Arabidopsis thaliana
Source AG Weber, Freiburg
Submitted by [http://2013.igem.org/Team:Freiburg Freiburg 2013]

Phytochrome B is a photoreceptor which detects red and far-red light. In Arabidopsis thaliana, Phytochrome B predominantly controls seedling establishment. It is a protein with a molecular mass of 125 kDa that is predominantly located in the cytoplasm. Its structure can be roughly divided in two parts: The N-terminal regulatory and photosensory part and the C-terminal regulatory part. The N-terminal part is covalently bound to phytochromibilin. Phytochromibilin is a linear tetrapyrol that undergoes conformational changes upon radiation of either red- or far red-light when bound to the phytochrome moiety. This conformational change is responsible for the photosensory properties of PhyB. [1]
Illumination with red light (660 nm wavelength) leads to binding of Phytochrome Interaction Factor 6 (PIF6). The interaction can be abolished by illumination with far-red light (740 nm) wavelength.
Team Freiburg 2013 uses Phy B to induce gene activation or repression via light stimulus. Therefore Phy B can be fused to effector domains like VP16 or KRAB.



Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 490
    Illegal BamHI site found at 572
    Illegal XhoI site found at 523
    Illegal XhoI site found at 542
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI site found at 739


Protein data table for BioBrick BBa_K1150004 automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)
 ATGGCCGGCATGGTTTCC ... GAGTTAGGTACCGGT
 ORF from nucleotide position -8 to 1956 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 
301 
401 
501 
601 		MAGMVSGVGGSGGGRGGGRGGEEEPSSSHTPNNRRGGEQAQSSGTKSLRPRSNTESMSKAIQQYTVDARLHAVFEQSGESGKSFDYSQSLKTTTYGSSVP
EQQITAYLSRIQRGGYIQPFGCMIAVDESSFRIIGYSENAREMLGIMPQSVPTLEKPEILAMGTDVRSLFTSSSSILLERAFVAREITLLNPVWIHSKNT
GKPFYAILHRIDVGVVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQALPGGDIKLLCDTVVESVRDLTGYDRVMVYKFHEDEHGEVVAESKRDDLEP
YIGLHYPATDIPQASRFLFKQNRVRMIVDCNATPVLVVQDDRLTQSMCLVGSTLRAPHGCHSQYMANMGSIASLAMAVIINGNEDDGSNVASGRSSMRLW
GLVVCHHTSSRCIPFPLRYACEFLMQAFGLQLNMELQLALQMSEKRVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAAFLYHGKYYPLGVAPSEV
QIKDVVEWLLANHADSTGLSTDSLGDAGYPGAAALGDAVCGMAVAYITKRDFLFWFRSHTAKEIKWGGAKHHPEDKDDGQRMHPRSSFQAFLEVVKSRSQ
PWETAEMDAIHSLQLILRDSFKESEAAMNSKVVDGVVQPCRDMAGEQGIDELGTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
None of the supported features appeared in the sequence
Amino acid composition:
Ala (A)53 (8.1%)
Arg (R)39 (6.0%)
Asn (N)15 (2.3%)
Asp (D)38 (5.8%)
Cys (C)12 (1.8%)
Gln (Q)33 (5.0%)
Glu (E)38 (5.8%)
Gly (G)58 (8.9%)
His (H)18 (2.7%)
Ile (I)33 (5.0%)
Leu (L)57 (8.7%)
Lys (K)24 (3.7%)
Met (M)24 (3.7%)
Phe (F)20 (3.1%)
Pro (P)29 (4.4%)
Ser (S)63 (9.6%)
Thr (T)30 (4.6%)
Trp (W)6 (0.9%)
Tyr (Y)18 (2.7%)
Val (V)47 (7.2%)
Amino acid counting
Total number:655
Positively charged (Arg+Lys):63 (9.6%)
Negatively charged (Asp+Glu):76 (11.6%)
Aromatic (Phe+His+Try+Tyr):62 (9.5%)
Biochemical parameters
Atomic composition:C3121H4952N886O967S36
Molecular mass [Da]:71513.2
Theoretical pI:5.80
Extinction coefficient at 280 nm [M-1 cm-1]:59820 / 60570 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):good (0.73)good (0.75)good (0.67)good (0.76)good (0.80)good (0.64)
Alignments (obtained from PredictProtein.org)
   There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours.
Predictions (obtained from PredictProtein.org)
   There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours.
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
If you have any questions, comments or suggestions, please leave us a comment.

References

[1] Lars-Oliver Essen, Jo Mailliet, and Jon Hughes 2008; Quail 2002


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Categories
Parameters
None