Part:BBa_K1796007
nifB from Paenibacillus sp. WLY78
essential for biosynthesis of the active-site nitrogenase cofactor and encodes a radical A-adenosylmethionine(SAM)-dependent enzyme that inserts the central carbon atom into the eight-Fe core of nifB cofactor(nifB-co).
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal EcoRI site found at 1156
- 12INCOMPATIBLE WITH RFC[12]Illegal EcoRI site found at 1156
- 21INCOMPATIBLE WITH RFC[21]Illegal EcoRI site found at 1156
- 23INCOMPATIBLE WITH RFC[23]Illegal EcoRI site found at 1156
- 25INCOMPATIBLE WITH RFC[25]Illegal EcoRI site found at 1156
Illegal AgeI site found at 129
Illegal AgeI site found at 1089
Illegal AgeI site found at 1444 - 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI.rc site found at 1261
Parameter of Protein
Number of amino acids: 499
Molecular weight: 54869.8
Theoretical pI: 6.64
Amino acid composition:
Ala (A) 46 9.2%
Arg (R) 35 7.0%
Asn (N) 17 3.4%
Asp (D) 23 4.6%
Cys (C) 16 3.2%
Gln (Q) 19 3.8%
Glu (E) 40 8.0%
Gly (G) 42 8.4%
His (H) 17 3.4%
Ile (I) 30 6.0%
Leu (L) 41 8.2%
Lys (K) 25 5.0%
Met (M) 11 2.2%
Phe (F) 13 2.6%
Pro (P) 25 5.0%
Ser (S) 27 5.4%
Thr (T) 17 3.4%
Trp (W) 2 0.4%
Tyr (Y) 13 2.6%
Val (V) 40 8.0%
Pyl (O) 0 0.0%
Sec (U) 0 0.0%
(B) 0 0.0%
(Z) 0 0.0%
(X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 63
Total number of positively charged residues (Arg + Lys): 60
Atomic composition:Carbon C 2398
Hydrogen H 3849
Nitrogen N 701
Oxygen O 719
Sulfur S 27
Formula: C2398H3849N701O719S27Total number of atoms: 7694
Extinction coefficients:Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient 31370
Abs 0.1% (=1 g/l) 0.572, assuming all pairs of Cys residues form cystines
Ext. coefficient 30370
Abs 0.1% (=1 g/l) 0.553, assuming all Cys residues are reduced
Estimated half-life:The N-terminal of the sequence considered is M (Met).
The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
>20 hours (yeast, in vivo).
>10 hours (Escherichia coli, in vivo).
Instability index:The instability index (II) is computed to be 43.03
This classifies the protein as unstable.
Aliphatic index: 87.96
Grand average of hydropathicity (GRAVY): -0.253
Aliphatic index: 92.50
Grand average of hydropathicity (GRAVY): -0.161
IGEM2018_Nanjing-China improve
The existing part, BBa_K1796007, is an essential component of the Paenibacillus sp. WLY78’s nitrogen fixation gene (nif) cluster arranged in the order of nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA, nifV. Instead of directly cloning WLY78 nifB using BBa_K1796007 as the template, a minimal nif cluster from Paenibacillus polymyxaCR1 that also contained nifB (nucleoid acid sequence similarity 96% as compared to WLY78 nifB) was chemically synthesized and incorporated into commercially available cloning vector pUC57. After that, CR1 nifB was obtained by PCR amplification using pUC57-nif as the template and subsequently introduced into pSB1C3 backbone through restriction enzyme digestion. Below, we discuss why we made such an improvement:
(1)Both nifB genes from WLY78 and CR1 contain unwanted restriction sites that can not meet the compatibility requirements of the iGEM Parts Guidelines. Therefore, elimination of these site through chemical synthesis is necessary.
(2) The complete genome of Paenibacillus polymyxa CR1has been thoroughly sequenced and deposited in NCBI with the accession number CP006941.2. Considering that there exist some other genes possessing regulatory function for the nif cluster, nifB of a bacterium with clear genetic background, such as Paenibacillus polymyxa CR1, may be more valuable for researchers of relevant field.
In addition, to test whether the nifB could express in gram-negative E. coli JM109</a> as a part of the nif cluster, pUC57-nif was inreoduced into JM109 via electroporation (Figure 1a). But before qRT-PCR determination, the function and strength of the native promoter in nif cluster (Pnif) were firstly tested in JM109 by fusing Dronpa as the reporter. T5 promoter (BBa_M50075) severed as control. As shown in Figure 1b, compared with T5 promoter, Pnif was much stronger in driving the expression of RFP and its expression pattern was constitutive. Transcriptional analysis was carried out afterward. As shown in Figure 2, Pnif was strong enough to drive the expression of each structure gene in the nif cluster including nifB though with different relative expression level.
Hopefully, the aforementioned improvements and relevant testing results can facilitate the utilization of the improved part for other iGEM team.
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