Coding

Part:BBa_K1159012

Designed by: Rosario CICCONE   Group: iGEM13_TU-Munich   (2013-05-17)

Secretory Catechol-2,3-dioxygenase (SERK-SigP_XylE) in RFC[25] N-Part

This part encodes for the enzyme catechol-2,3-dioxygenase (metapyrocatechase), which converts catechol to the bright yellow product 2-hydroxy-cis,cis-muconic semialdehyde. This part is fused with a N-terminal signal peptide for secretion (signal peptide from SERK Receptor of Physcomitrella patens). This construct is flanked by RFC[25] N-part prefix and suffix. Note: This means only protein fusions to the C-terminus of this part is possible, adding promoters (typically RFC[10]) into the prefix or terminators/IRES (typically RFC[10]) into the suffix of this part is nevertheless possible.

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 N-Part using the stop codon in the suffix, so ACCGGT was added (in italics) to the 3' end: (underlined part encodes the protein)
 AACAATGCCTGGT ... GTGCTGACCACCGGT
 ORF from nucleotide position 5 to 1030 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)

101 
201 
301 
MPGEVAWWRPLFLIALMPIGVLSNAEGDALNTTGNKGVMRPGHVQLRVLDMSKALEHYVELLGLIEMDRDDQGRVYLKAWTEVDKFSLVLREADEPGMDF
MGFKVVDEDALRQLERDLMAYGCAVEQLPAGELNSCGRRVRFQAPSGHHFELYADKEYTGKWGLNDVNPEAWPRDLKGMAAVRFDHALMYGDELPATYDL
FTKVLGFYLAEQVLDENGTRVAQFLSLSTKAHDVAFIHHPEKGRLHHVSFHLETWEDLLRAADLISMTDTSIDIGPTRHGLTHGKTIYFFDPSGNRNEVF
CGGDYNYPDHKPVTWTTDQLGKAIFYHDRILNERFMTVLTTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
RFC25 scar (shown in bold): 33 to 34
Amino acid composition:
Ala (A)25 (7.3%)
Arg (R)20 (5.8%)
Asn (N)11 (3.2%)
Asp (D)28 (8.2%)
Cys (C)3 (0.9%)
Gln (Q)8 (2.3%)
Glu (E)23 (6.7%)
Gly (G)29 (8.5%)
His (H)15 (4.4%)
Ile (I)10 (2.9%)
Leu (L)39 (11.4%)
Lys (K)14 (4.1%)
Met (M)12 (3.5%)
Phe (F)17 (5.0%)
Pro (P)15 (4.4%)
Ser (S)11 (3.2%)
Thr (T)20 (5.8%)
Trp (W)7 (2.0%)
Tyr (Y)12 (3.5%)
Val (V)23 (6.7%)
Amino acid counting
Total number:342
Positively charged (Arg+Lys):34 (9.9%)
Negatively charged (Asp+Glu):51 (14.9%)
Aromatic (Phe+His+Try+Tyr):51 (14.9%)
Biochemical parameters
Atomic composition:C1742H2658N472O507S15
Molecular mass [Da]:38806.0
Theoretical pI:5.28
Extinction coefficient at 280 nm [M-1 cm-1]:56380 / 56568 (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 (0.70)acceptable (0.55)good (0.65)excellent (0.83)good (0.78)
Alignments (obtained from PredictProtein.org)
SwissProt:P06622 (100% identity on 306 AAs), P27887 (94% identity on 306 AAs)
TrEML:D2XKL2 (100% identity on 306 AAs), G5DRD2 (100% identity on 215 AAs), J9ZVS6 (100% identity on 270 AAs), J9ZVW6 (100% identity on 270 AAs), J9ZX53 (100% identity on 270 AAs), Q38Q96 (100% identity on 293 AAs), Q7AXV1 (100% identity on 306 AAs), Q7BH44 (100% identity on 306 AAs), J9ZVF5 (99% identity on 270 AAs), Q5EGN5 (99% identity on 237 AAs)
PDB:1mpy (100% identity on 306 AAs), 3hpv (48% identity on 296 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:cytosol (100%)
Bacteria:cytosol (84%)
Eukarya:secreted (43%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:GO:0019439 (49%), GO:0055114 (35%)
 
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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Categories
Parameters
None