Difference between revisions of "Part:BBa K5246001"

Revision as of 06:41, 29 September 2024

CB2/CB2A HfsA Part of export protein complex

Introduction

Usage and Biology

Gene HfsA from Caulobacter crescentus encodes a protein of 502 amino acids from the complex that, in combination with HfsB, is responsible for the controlled polymerization of holdfast polysaccharides. HfsA is a polysaccharide copolymerize Wzz

This part is also a part of the holdfast export operon BBa_K5246044 and a part of full polymerization and export operon BBa_K5246046 .

Sequence and Features

Bioinformatical characterization

Bioinformatic analysis

Conservative Domain Database analysis revealed that the HfsA protein contains domains characteristic of the GumC superfamily, which typically function in exopolysaccharide export within the cell wall or membrane. Additionally, it shows significant similarity to the PEP-CTERM superfamily, proteins that are generally involved in determining polysaccharide chain length.

NCBI protein BLAST analysis revealed significant similarities between HfsA and a capsular polysaccharide biosynthesis protein from the ABC transporter family of Caldimonas thermodepolymerans. Using the DeepTMHMM tool to analyze its transmembrane structure, it was predicted that HfsA spans the membrane twice, embedding itself firmly in the cell envelope.

With AlphaFold3, we assessed different configurations of HfsA subunits, focusing on ipTM and pTM scores. 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. We hypothesize that the HfsA transmembrane protein consists of 8 subunits with confidence scores of ipTM = 0.72 and pTM = 0.73 (Fig.1).

Based on this data, we hypothesize that HfsA is a transmembrane protein that exports polysaccharides from the cell. Similar findings were proposed by earlier research. [1][2][3][4]

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References

1. Kurtz, H.D. and Smith, J. (1994) ‘The Caulobacter crescentushold fast: Identification of holdfast attachment complex genes’, FEMS Microbiology Letters, 116(2), pp. 175–182. doi:10.1111/j.1574-6968.1994.tb06697.x.
2. Javens, J. et al. (2013) ‘Bypassing the need for subcellular localization of a polysaccharide export‐anchor complex by overexpressing its protein subunits’, Molecular Microbiology, 89(2), pp. 350–371. doi:10.1111/mmi.12281.
3. 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.
4. Toh, E., Kurtz, H.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. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2580695/