Difference between revisions of "Part:BBa K5246015"
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===Usage and Biology===
 
===Usage and Biology===
  
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Gene HfsC from Hirschia baltica, encoding a protein of 454 amino acids polymerases repeats of monomers into a mature holdfast polymer. Deletion of polysaccharide polymerase gene hfsC in C.Crescentus didn't cause holdfast synthesis defects, because of its paralogue - HfsI. Double mutants of HfsC and HfsI cause severe holfast synthesis defects
+
Gene HfsC from Hirschia baltica, encoding a protein of 454 amino acids polymerases repeats of monomers into a mature holdfast polymer. Deletion of polysaccharide polymerase gene hfsC in C.Crescentus didn't cause holdfast synthesis defects because of its paralogue - HfsI. Double mutants of HfsC and HfsI cause severe holdfast synthesis defects
  
 
===Sequence and Features===
 
===Sequence and Features===
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===Experimental characterization===
 
===Experimental characterization===
  
 +
====Bioinformatic analysis====
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 +
CDD analysis showed that only part of the protein resembles established conservative domains. The predicted domain is part of the O-antigen ligase family, which is a group of proteins responsible for outer membrane lipopolysaccharide synthesis in <i>E. coli</i>.
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 +
Protein BLAST also showed partial similarities with E.Coli O-antigen ligases suggested by the CDD analysis.
 +
 +
DeepTMHMM predicted that the protein is embedded in the membrane, crossing it approximately 12 times. This prediction is supported by structural evidence from AlphaFold 3, which shows 12 helices. 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.
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Considering the data, HfsC is most probably a membrane protein that functions as a polysaccharide ligase due to its similarity to O-antigen ligase; this hypothesis is further supported by earlier research. [1][2]
  
 
===References===
 
===References===
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1. Smith, C.S. et al. (2003a) ‘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. 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 10:35, 28 September 2024


HB HfsC Polysaccharide polymerase

Introduction

Usage and Biology

Gene HfsC from Hirschia baltica, encoding a protein of 454 amino acids polymerases repeats of monomers into a mature holdfast polymer. Deletion of polysaccharide polymerase gene hfsC in C.Crescentus didn't cause holdfast synthesis defects because of its paralogue - HfsI. Double mutants of HfsC and HfsI cause severe holdfast synthesis defects

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
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 889
  • 1000
    COMPATIBLE WITH RFC[1000]


Functional Parameters

Experimental characterization

Bioinformatic analysis

CDD analysis showed that only part of the protein resembles established conservative domains. The predicted domain is part of the O-antigen ligase family, which is a group of proteins responsible for outer membrane lipopolysaccharide synthesis in E. coli.

Protein BLAST also showed partial similarities with E.Coli O-antigen ligases suggested by the CDD analysis.

DeepTMHMM predicted that the protein is embedded in the membrane, crossing it approximately 12 times. This prediction is supported by structural evidence from AlphaFold 3, which shows 12 helices. 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.

Considering the data, HfsC is most probably a membrane protein that functions as a polysaccharide ligase due to its similarity to O-antigen ligase; this hypothesis is further supported by earlier research. [1][2]

References

1. Smith, C.S. et al. (2003a) ‘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. 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.