Difference between revisions of "Part:BBa K5246002"
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<partinfo>BBa_K5246002 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K5246002 SequenceAndFeatures</partinfo>
  
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===Functional Parameters===
 
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<partinfo>BBa_K5246002 parameters</partinfo>
 
  
 
===Experimental characterization===
 
===Experimental characterization===
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====Bioinformatic analysis====
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Conservative Domain Database analysis revealed that the HfsB protein contains domains characteristic of the CpaE-like family. Members of this group contain proteins similar to the cpaE protein of the Caulobacter pilus assembly. Additionally, it resembles the eps_fam family, which typically describes the capsular exopolysaccharide proteins in bacteria. A number of these proteins regulate the exopolysaccharide biosynthesis (EPS).
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NCBI protein BLAST analysis identified similarities between HfsB and several membrane-associated tyrosine-protein kinases.
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Using the DeepTMHMM tool to analyze its transmembrane structure, it was predicted that HfsB does not wholly cross the membrane. Instead, it is positioned on the inner side, only associated with the membrane, congruous with earlier hypotheses proposed in the literature.
 +
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When analyzed independently, protein structure prediction using AlphaFold 3 produced unclear results for HfsB. Since HfsB is part of the polysaccharide export complex, we attempted to fold it with HfsA, significantly improving the outcome. HfsB only folds correctly in the presence of HfsA, supporting the hypothesis that these two proteins function together as a single export unit. A pTM score above 0.5 suggests that the predicted overall structure may closely resemble the true protein fold, while ipTM indicates the accuracy of the subunit positioning within the complex. Values higher than 0.8 represent confident, high-quality predictions (Fig.1).
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In summary, HfsB is probably a component of the membrane polysaccharide export apparatus that closely interacts with HfsA and is required for holdfast synthesis. [1][2][3]
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<center> https://static.igem.wiki/teams/5246/registry/hfsb.png </center>
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<center> <b> Fig. 1. </b> Alphafold 3 structure  </center>
  
  
 
===References===
 
===References===
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1. Smith, C.S. et al. (2003) ‘Identification of genes required for synthesis of the adhesive holdfast in            Caulobacter crescentus’, Journal of Bacteriology, 185(4), pp. 1432–1442. doi:10.1128/jb.185.4.1432-1442.2003.
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<br>
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2. Brown, P.J.B. et al. (2008) ‘Complex regulatory pathways coordinate cell-cycle progression and development in Caulobacter Crescentus’, Advances in Microbial Physiology, pp. 1–101. doi:10.1016/s0065-2911(08)00001-5.
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<br>
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3. Toh, E., Kurtz, Harry D. and Brun, Y.V. (2008) ‘Characterization of the Caulobacter crescentus holdfast polysaccharide biosynthesis pathway reveals significant redundancy in the initiating glycosyltransferase and polymerase steps’, Journal of Bacteriology, 190(21), pp. 7219–7231. doi:10.1128/jb.01003-08.

Revision as of 13:11, 27 September 2024


CB2/CB2A HfsB Part of export protein complex

Introduction

Usage and Biology

Gene HfsB from Caulobacter crescentus that encodes a protein from complex that in combination with HfsA is responsible for controlled polymerisation of holdfast pollysaccharide. HfsB is a polysaccharide secretion autokinase

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 127
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 127
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 127
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 127
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 127
    Illegal NgoMIV site found at 413
  • 1000
    COMPATIBLE WITH RFC[1000]


Experimental characterization

Bioinformatic analysis

Conservative Domain Database analysis revealed that the HfsB protein contains domains characteristic of the CpaE-like family. Members of this group contain proteins similar to the cpaE protein of the Caulobacter pilus assembly. Additionally, it resembles the eps_fam family, which typically describes the capsular exopolysaccharide proteins in bacteria. A number of these proteins regulate the exopolysaccharide biosynthesis (EPS). NCBI protein BLAST analysis identified similarities between HfsB and several membrane-associated tyrosine-protein kinases. Using the DeepTMHMM tool to analyze its transmembrane structure, it was predicted that HfsB does not wholly cross the membrane. Instead, it is positioned on the inner side, only associated with the membrane, congruous with earlier hypotheses proposed in the literature.

When analyzed independently, protein structure prediction using AlphaFold 3 produced unclear results for HfsB. Since HfsB is part of the polysaccharide export complex, we attempted to fold it with HfsA, significantly improving the outcome. HfsB only folds correctly in the presence of HfsA, supporting the hypothesis that these two proteins function together as a single export unit. A pTM score above 0.5 suggests that the predicted overall structure may closely resemble the true protein fold, while ipTM indicates the accuracy of the subunit positioning within the complex. Values higher than 0.8 represent confident, high-quality predictions (Fig.1).

In summary, HfsB is probably a component of the membrane polysaccharide export apparatus that closely interacts with HfsA and is required for holdfast synthesis. [1][2][3]

hfsb.png
Fig. 1. Alphafold 3 structure


References

1. Smith, C.S. et al. (2003) ‘Identification of genes required for synthesis of the adhesive holdfast in Caulobacter crescentus’, Journal of Bacteriology, 185(4), pp. 1432–1442. doi:10.1128/jb.185.4.1432-1442.2003.
2. Brown, P.J.B. et al. (2008) ‘Complex regulatory pathways coordinate cell-cycle progression and development in Caulobacter Crescentus’, Advances in Microbial Physiology, pp. 1–101. doi:10.1016/s0065-2911(08)00001-5.
3. Toh, E., Kurtz, Harry D. and Brun, Y.V. (2008) ‘Characterization of the Caulobacter crescentus holdfast polysaccharide biosynthesis pathway reveals significant redundancy in the initiating glycosyltransferase and polymerase steps’, Journal of Bacteriology, 190(21), pp. 7219–7231. doi:10.1128/jb.01003-08.