Difference between revisions of "Part:BBa K5246006"
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HfsF is a flippase with domains, partly similar to some polysaccharide synthesis pathway proteins in bacteria, as it was shown by CDD analysis. | HfsF is a flippase with domains, partly similar to some polysaccharide synthesis pathway proteins in bacteria, as it was shown by CDD analysis. | ||
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Protein BLAST indicates high similarities to MOP superfamily flippases involved in peptidoglycan synthesis. | Protein BLAST indicates high similarities to MOP superfamily flippases involved in peptidoglycan synthesis. | ||
DeepTMHMM predictions suggest that the protein is located in the membrane, spanning it multiple times. | DeepTMHMM predictions suggest that the protein is located in the membrane, spanning it multiple times. | ||
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Considering high AlphaFold 3 structure confidence scores, it seems probable that hfsF is made of alpha 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 (Fig.1). | Considering high AlphaFold 3 structure confidence scores, it seems probable that hfsF is made of alpha 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 (Fig.1). | ||
Revision as of 13:41, 27 September 2024
CB2/CB2A HfsF Flippase
Introduction
Usage and Biology
Encodes an integral membrane protein of 480 amino acids with 14 predicted transmembrane helices. Possesses similarities to Wzx flippases (formerly known as RfbX) that catalyze the translocation of undecaprenol diphosphate-linked K-repeating units formed at the cytoplasmic side of the inner membrane across this membrane.
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal PstI site found at 1033
- 12INCOMPATIBLE WITH RFC[12]Illegal PstI site found at 1033
- 21INCOMPATIBLE WITH RFC[21]Illegal BamHI site found at 93
- 23INCOMPATIBLE WITH RFC[23]Illegal PstI site found at 1033
- 25INCOMPATIBLE WITH RFC[25]Illegal PstI site found at 1033
Illegal NgoMIV site found at 343
Illegal NgoMIV site found at 451
Illegal NgoMIV site found at 733
Illegal NgoMIV site found at 790
Illegal NgoMIV site found at 834
Illegal NgoMIV site found at 865
Illegal NgoMIV site found at 1089
Illegal AgeI site found at 151 - 1000COMPATIBLE WITH RFC[1000]
Experimental characterization
Bioinformatic analysis
HfsF is a flippase with domains, partly similar to some polysaccharide synthesis pathway proteins in bacteria, as it was shown by CDD analysis.
Protein BLAST indicates high similarities to MOP superfamily flippases involved in peptidoglycan synthesis. DeepTMHMM predictions suggest that the protein is located in the membrane, spanning it multiple times.
Considering high AlphaFold 3 structure confidence scores, it seems probable that hfsF is made of alpha 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 (Fig.1).
All in all, HfsF is a flippase located in the membrane that is responsible for oligosaccharide transfer from the cytoplasmic to the periplasmic side of the inner membrane. This flippase is similar to flippases involved in peptidoglycan synthesis. Our results align with prior studies. [1][2][3]
References
1. 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.
2. Hardy, G.G. et al. (2018) ‘Mutations in sugar-nucleotide synthesis genes restore holdfast polysaccharide anchoring to Caulobacter crescentus holdfast anchor mutants’, Journal of Bacteriology, 200(3). doi:10.1128/jb.00597-17.
3. Hershey, D.M., Fiebig, A. and Crosson, S. (2019) ‘A genome-wide analysis of adhesion in Caulobacter crescentus identifies new regulatory and biosynthetic components for holdfast assembly’, mBio, 10(1). doi:10.1128/mbio.02273-18.