Coding

Part:BBa_K1150007

Designed by: Freiburg 2013   Group: iGEM13_Freiburg   (2013-09-16)
Revision as of 00:50, 9 October 2013 by TU Munich (Talk | contribs) (→‎Sequence and Features)

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COP1

COP1
Function interaction partner of

UVR8,reacts to UVB light

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

Sunlight is essential for plants: Not only as an energy source but also as information for their growth cycle. Therefore they need mechanisms to detect different light wavelengths. E3-ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is the interaction partner of ultraviolet B (UVB) light receptor UVR8 [1]. The ubiqutin ligase activity of this COP1 is eliminated, only the WD40 domain remains. This minimizes the risk of cross talk in mammalian cells [2].


Biology and Usage

When UVB light is perceived by the UVR8 photoreceptor it monomerizes and therefore changes in its open confuguration. Then it recruits COP1. This is a signal for plant cells to react to UVB light, for example with photomorphogenesis [3]. Freiburg 2013 used this part to engineer a UVB light induced mechanism to activate gene expression. You need a combination of these BioBricks: Cas9-UVR8, COP1-VP16, RNAimer


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 787
    Illegal BsaI.rc site found at 864
    Illegal SapI.rc site found at 376


Protein data table for BioBrick BBa_K1150007 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)
 ATGGCCGGCATGTATAGC ... CTCGCTGCGACCGGT
 ORF from nucleotide position -8 to 1029 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 
301 		MAGMYSNGLADFQSVLTTFTRYSRLRVIAEIRHGDIFHSANIVSSIEFDRDDELFATAGVSRCIKVFDFSSVVNEPADMQCPIVEMSTRSKLSCLSWNKH
EKNHIASSDYEGIVTVWDVTTRQSLMEYEEHEKRAWSVDFSRTEPSMLVSGSDDCKVKVWCTRQEASVINIDMKANICCVKYNPGSSNYIAVGSADHHIH
YYDLRNISQPLHVFSGHKKAVSYVKFLSNNELASASTDSTLRLWDVKDNLPVRTFRGHTNEKNFVGLTVNSEYLACGSETNEVYVYHKEITRPVTSHRFG
SPDMDDAEEEAGSYFISAVCWKSDSPTMLTANSQGTIKVLVLAATG*
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)23 (6.6%)
Arg (R)17 (4.9%)
Asn (N)18 (5.2%)
Asp (D)22 (6.4%)
Cys (C)9 (2.6%)
Gln (Q)6 (1.7%)
Glu (E)22 (6.4%)
Gly (G)16 (4.6%)
His (H)13 (3.8%)
Ile (I)18 (5.2%)
Leu (L)20 (5.8%)
Lys (K)17 (4.9%)
Met (M)9 (2.6%)
Phe (F)14 (4.0%)
Pro (P)9 (2.6%)
Ser (S)41 (11.8%)
Thr (T)22 (6.4%)
Trp (W)6 (1.7%)
Tyr (Y)13 (3.8%)
Val (V)31 (9.0%)
Amino acid counting
Total number:346
Positively charged (Arg+Lys):34 (9.8%)
Negatively charged (Asp+Glu):44 (12.7%)
Aromatic (Phe+His+Try+Tyr):46 (13.3%)
Biochemical parameters
Atomic composition:C1703H2632N470O535S18
Molecular mass [Da]:38827.5
Theoretical pI:5.71
Extinction coefficient at 280 nm [M-1 cm-1]:52370 / 52933 (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 (0.73)good (0.67)good (0.74)good (0.78)good (0.68)
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] Rizzini L., Favory J.-J., Cloix C., Faggionato D., O'Hara A., Kaiserli E., Baumeister R., Schäfer E., Nagy F., Jenkins G. I., Ulm R. (2011). Perception of UV-B by the Arabidopsis UVR8 protein. Science 332

[2] Müller K., Engesser R., Schulz S., Steinberg T., Tomakidi P., Weber C. C., Ulm R., Timmer J., Zurbriggen M. D., Weber W. (2013). Multi-chromatic control of mammalian gene expression and signaling. Nucleic Acids Research Vol. 41, No. 12

[3] Favory J.-J., Stec A., Gruber H., Rizzini L., Oravecz A., Funk M., Albert A., Cloix C., Jenkins G. I., Oakeley E. J., Seidlitz H. K., Nagy F., Ulm R. (2009). Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. The EMBO Journal 28, 591-600


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