BBa_B0032
1
BBa_B0032
RBS.3 (medium) -- derivative of BBa_0030
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
Released HQ 2013
Weak1 RBS based on Ron Weiss thesis. Strength is considered relative to <bb_part>BBa_B0030</bb_part>, <bb_part>BBa_B0031</bb_part>, <bb_part>BBa_B0033</bb_part>.
false
true
_41_44_48_46_1_
0
24
7
In stock
false
Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix ("RBS-2" in figure 4-14 of thesis). <P>
Contact info for this part: <a href="mailto:(bchow@media.mit.edu)">Brian Chow</a>
true
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
annotation1710
1
RBS
range1710
1
7
10
annotation7027
1
BBa_B0032
range7027
1
1
13
annotation1709
1
RBS-3\Weak
range1709
1
1
13
BBa_K608006
1
BBa_K608006
medium Promoter , medium RBS
2011-09-14T11:00:00Z
2015-05-08T01:12:52Z
composite
Released HQ 2013
medium Promotor , medium RBS
false
false
_780_
0
9115
9
In stock
false
composite
false
Julia M??ller
component2128659
1
BBa_J23110
component2128661
1
BBa_B0032
annotation2128659
1
BBa_J23110
range2128659
1
1
35
annotation2128661
1
BBa_B0032
range2128661
1
44
56
BBa_J23110
1
BBa_J23110
constitutive promoter family member
2006-08-16T11:00:00Z
2015-08-31T04:08:40Z
Later
Later
false
true
_52_
0
483
95
In stock
true
N/A
true
John Anderson
BBa_K1909008
1
BBa_K1909008
Medium Anderson / mTaz
2016-10-13T11:00:00Z
2016-10-14T11:44:03Z
Composite Part
Coming soon
false
false
_2375_
29525
29525
9
false
Coming soon
false
Daniel Wedemeyer
component2507591
1
BBa_K608006
component2507597
1
BBa_K1909002
annotation2507591
1
BBa_K608006
range2507591
1
1
56
annotation2507597
1
BBa_K1909002
range2507597
1
63
1514
BBa_K1909002
1
mTaz
mTaz (Taz-derived mDAP receptor)
2016-10-13T11:00:00Z
2016-10-14T10:47:39Z
mTaz is based on the Tar-EnvZ chimeric receptor which is capable of detecting aspartate in the medium as described by Utsumi et al. 1989. Tar, or methyl-accepting chemotaxis protein II, is a signal transducer in Escherichia coli chemotaxis and is activated upon the recognition of aspartate. Tar is sensitive to mutations altering its ligand specificity which sometimes results in recognizing other amino acids. EnvZ is a part of the well-studied and commonly used two-component system EnvZ/OmpR in E. coli, offering a simple way of signal transduction. Its periplasmic domain was shown to be exchangeable with different sensor domains e.g. Tar/EnvZ chimeric receptor capable of detecting aspartate in the medium.
Coming as soon as we validated mTaz.
false
false
_2375_
29525
29525
9
false
meso-2,6-Diaminopimelic acid (mDAP) is a non-proteinogenic amino acid that is synthesized and se-creted by Chlamydia trachomatis. mDAP has a relatively high chemical similarity to aspartate, sharing a Tanimoto coefficient of T=0.8 in a molecular fingerprint analysis [T<0: chemically very different struc-tures; T=1: identity]. As a proof of concept, a molecular docking model proposes few mutations which would change the Tar specificity towards mDAP. As input for molecular docking we used the crys-tal structure of the ligand binding domain of Tar bound to aspartate (PDB: 4Z9H).
As a base for the part sequence, the BioBrick representation of the original Taz, BBa_C0082, was used. The BBa_C0082 BioBrick features a small part of the vector (64 nucleotides) it was derived from on its 3??? end, which we have removed along with the stop codon inside the Part for further fusion protein de-sign in RFC 12, 21, 23 and 25 assembly standards.
We used the Glide algorithm, Maestro and the Schrodinger Suite for molecular docking of aspartate and mDAP to the Tar ligand binding domain (PDB: 4Z9H). Because of its structural similarity to aspartate, mDAP showed some affinity to the native Tar aspartate binding site (Table 1). Since mDAP is larger than aspartate, Y149 led to structural interference, not allowing mDAP to fully enter the binding site. To create the additional space needed for mDAP binding, we substituted Y149 with smaller amino acids. The best results were obtained with serine. Because of the additional size of mDAP, the bigger challenge was to reduce the affinity of aspartate rather than to raise the affinity of mDAP. We identified R64 as a key residue for aspartate binding which hovewer was not needed to bind mDAP. To minimally interfere with folding and function we performed a constitutive substitution and substituted it with lysine, creating the R64K Y149S double mutant called mTaz hereafter. Using mTaz, a higher docking score was achieved for mDAP than for aspartate (Table 1).
false
Daniel Wedemeyer, Alp Mirdoğan
annotation2506923
1
R64K
range2506923
1
190
192
annotation2506924
1
Y149S
range2506924
1
445
447
annotation2506922
1
EnvZ
range2506922
1
766
1452
annotation2506919
1
Tar
range2506919
1
1
765
annotation2506915
1
mTaz
range2506915
1
1
1452
BBa_K1909008_sequence
1
tttacggctagctcagtcctaggtacaatgctagctactagagtcacacaggaaagtactagatgattaaccgtatccgcgtagtcacgctgttggtaatggtgctgggggtattcgcactgttacagcttatttccggcagtctgtttttttcttcccttcaccatagccagaagagctttgtggtttccaatcaattacgggaacagcagggcgagctgacgtcaacctgggatttaatgctgcaaacgaaaattaacctgagtcgttcagcggtacggatgatgatggattcctccaatcaacaaagtaacgccaaagttgaattgctcgatagcgccaggaaaacattggcgcaggcagcgacgcattataaaaaattcaaaagcatggcaccgttacctgaaatggtcgctaccagtcgtaatattgatgaaaaatataaaaactattacacagcgttaactgaactgattgattatctcgattatggcaatactggagcttctttcgctcagccaacccagggaatgcaaaatgcaatgggcgaagcgtttgctcagtacgccctcagcagtgaaaaactgtatcgcgatatcgtcactgacaacgcagatgattaccgatttgcccagtggcaactggcggttatcgcgctggtggtggtattgattctgctggtggcgtggtacggcattcgccgtatgttgcttactccgctggcaaaaattattgctcacattcgcgaaatcgccggtggtaacctggcgaataccctgaccattgacgggcgcagtgaaatgggcgacctggcgcagagcgtttcacatatggcggctggtgttaagcaactggcggatgaccgcacgctgctgatggcgggggtaagtcacgacttgcgcacgccgctgacgcgtattcgcctggcgactgagatgatgagcgagcaggatggctatctggcagaatcgatcaataaagatatcgaagagtgcaacgccatcattgagcagtttatcgactacctgcgcaccgggcaggagatgccgatggaaatggcggatcttaatgcagtactcggtgaggtgattgctgccgaaagtggctatgagcgggaaattgaaaccgcgctttaccccggcagcattgaagtgaaaatgcacccgctgtcgatcaaacgcgcggtggcgaatatggtggtcaacgccgcccgttatggcaatggctggatcaaagtcagcagcggaacggagccgaatcgcgcctggttccaggtggaagatgacggtccgggaattgcgccggaacaacgtaagcacctgttccagccgtttgtccgcggcgacagtgcgcgcaccattagcggcacgggattagggctggcaattgtgcagcgtatcgtggataaccataacgggatgctggagcttggcaccagcgagcggggcgggctttccattcgcgcctggctgccagtgccggtaacgcgggcgcagggcacgacaaaagaaggg
BBa_K608006_sequence
1
tttacggctagctcagtcctaggtacaatgctagctactagagtcacacaggaaag
BBa_B0032_sequence
1
tcacacaggaaag
BBa_J23110_sequence
1
tttacggctagctcagtcctaggtacaatgctagc
BBa_K1909002_sequence
1
atgattaaccgtatccgcgtagtcacgctgttggtaatggtgctgggggtattcgcactgttacagcttatttccggcagtctgtttttttcttcccttcaccatagccagaagagctttgtggtttccaatcaattacgggaacagcagggcgagctgacgtcaacctgggatttaatgctgcaaacgaaaattaacctgagtcgttcagcggtacggatgatgatggattcctccaatcaacaaagtaacgccaaagttgaattgctcgatagcgccaggaaaacattggcgcaggcagcgacgcattataaaaaattcaaaagcatggcaccgttacctgaaatggtcgctaccagtcgtaatattgatgaaaaatataaaaactattacacagcgttaactgaactgattgattatctcgattatggcaatactggagcttctttcgctcagccaacccagggaatgcaaaatgcaatgggcgaagcgtttgctcagtacgccctcagcagtgaaaaactgtatcgcgatatcgtcactgacaacgcagatgattaccgatttgcccagtggcaactggcggttatcgcgctggtggtggtattgattctgctggtggcgtggtacggcattcgccgtatgttgcttactccgctggcaaaaattattgctcacattcgcgaaatcgccggtggtaacctggcgaataccctgaccattgacgggcgcagtgaaatgggcgacctggcgcagagcgtttcacatatggcggctggtgttaagcaactggcggatgaccgcacgctgctgatggcgggggtaagtcacgacttgcgcacgccgctgacgcgtattcgcctggcgactgagatgatgagcgagcaggatggctatctggcagaatcgatcaataaagatatcgaagagtgcaacgccatcattgagcagtttatcgactacctgcgcaccgggcaggagatgccgatggaaatggcggatcttaatgcagtactcggtgaggtgattgctgccgaaagtggctatgagcgggaaattgaaaccgcgctttaccccggcagcattgaagtgaaaatgcacccgctgtcgatcaaacgcgcggtggcgaatatggtggtcaacgccgcccgttatggcaatggctggatcaaagtcagcagcggaacggagccgaatcgcgcctggttccaggtggaagatgacggtccgggaattgcgccggaacaacgtaagcacctgttccagccgtttgtccgcggcgacagtgcgcgcaccattagcggcacgggattagggctggcaattgtgcagcgtatcgtggataaccataacgggatgctggagcttggcaccagcgagcggggcgggctttccattcgcgcctggctgccagtgccggtaacgcgggcgcagggcacgacaaaagaaggg
igem2sbol
1
iGEM to SBOL conversion
Conversion of the iGEM parts registry to SBOL2.1
Chris J. Myers
James Alastair McLaughlin
2017-03-06T15:00:00.000Z