Coding

Part:BBa_K1159200

Designed by: Dong-Jiunn Jeffery TRUONG   Group: iGEM13_TU-Munich   (2013-09-14)
Revision as of 11:24, 12 October 2013 by Earthnut (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.

Experiments

Figure 1: Schematic of the working mechanism of post-translational non-canonical protein fusion using the SpyTag/SpyCatcher system

Proper funtion of the construct was verified in a pulldown assay using 10 μM of SpyCatcher with N-terminal HisTag which was incubated with 5 μM of C-terminal spytagged SYFP2 for 1 h in PBS. Afterwards HisTag beads were added to bind the fusion product, resulting in a decrease of spytagged SYFP2 in the supernatant. The results of this assay are shown in Figure 2. The results show that after one hour at room temeperature, a two fold change in relative absorbance was observed. This verifies that the construct is working as intended.

Figure 2: Results of the pulldown assay for the SpyTag/SpyCatcher system.

Reference

http://www.ncbi.nlm.nih.gov/pubmed/22366317 Zakeri et al., 2012 Zakeri B, Fierer JO, Celik E, Chittock EC, Schwarz-Linek U, Moy VT, Howarth M. (2012). Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proc Natl Acad Sci U S A. 20;109(12)


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.
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