Coding

Part:BBa_K1159200

Designed by: Dong-Jiunn Jeffery TRUONG   Group: iGEM13_TU-Munich   (2013-09-14)
Revision as of 19:53, 8 October 2013 by JohannaB (Talk | contribs)

Splitted and engineered N-terminal FbaB for isopeptide bound formation (SpyCatcher) in RFC[25]

This part codes for a protein that recognizes and forms a covalent isopeptide bound to a oligopeptide. That oligopeptide can be found under BBa_K1159201. In contrast to the original SpyCatcher this part only contains the essential part for forming isopeptide bounds and does not contain a N-terminal His-tag and TEV cleavage site. Furthermore two amino acids were exchanged to improve the function, Ile34 was replaced by Glu34 which enhances the reaction rate, also the exposed hydrophobic redidue Met69 was replaced by Tyr69. This part is flanked by RFC[25] pre- and suffix for further protein fusions.

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
    COMPATIBLE WITH RFC[1000]

Protein data table for BioBrick BBa_ 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)
 ATGGCCGGCGTTGATACC ... GCTCATATTACCGGT
 ORF from nucleotide position -8 to 345 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 		MAGVDTLSGLSSEQGQSGDMTIEEDSATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAAPDGYEVATAITFTVNEQ
GQVTVNGKATKGDAHITG*
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)10 (8.5%)
Arg (R)2 (1.7%)
Asn (N)2 (1.7%)
Asp (D)10 (8.5%)
Cys (C)0 (0.0%)
Gln (Q)5 (4.2%)
Glu (E)9 (7.6%)
Gly (G)14 (11.9%)
His (H)2 (1.7%)
Ile (I)6 (5.1%)
Leu (L)5 (4.2%)
Lys (K)8 (6.8%)
Met (M)3 (2.5%)
Phe (F)4 (3.4%)
Pro (P)2 (1.7%)
Ser (S)10 (8.5%)
Thr (T)14 (11.9%)
Trp (W)1 (0.8%)
Tyr (Y)4 (3.4%)
Val (V)7 (5.9%)
Amino acid counting
Total number:118
Positively charged (Arg+Lys):10 (8.5%)
Negatively charged (Asp+Glu):19 (16.1%)
Aromatic (Phe+His+Try+Tyr):11 (9.3%)
Biochemical parameters
Atomic composition:C543H848N144O192S3
Molecular mass [Da]:12561.7
Theoretical pI:4.49
Extinction coefficient at 280 nm [M-1 cm-1]:11460 / 11460 (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):excellent (0.83)good (0.76)good (0.78)good (0.80)good (0.78)good (0.67)
Alignments (obtained from PredictProtein.org)
SwissProt: -
TrEML:Q879P6 (97% identity on 114 AAs), Q8G9G1 (97% identity on 114 AAs)
PDB:2x5p (96% identity on 93 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:secreted (100%)
Bacteria:secreted (26%)
Eukarya:cytosol (45%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology: -
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
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.


[edit]
Categories
Parameters
None