Diversity and sequence motifs of the bacterial SecA protein motor

https://doi.org/10.1016/j.bbamem.2020.183319Get rights and content
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Highlights

  • We established a database of 425 curated SecA sequences, performed unsupervised sequence analyses.

  • We combined clustering and phylogeny information to identify motifs of PBD and NBD1.

  • SecA sequences have remarkable diversity of their length, estimated charge, and PBD.

  • N-terminus has conserved features with potential role in membrane anchoring.

Abstract

SecA is an essential component of the Sec protein secretion pathway in bacteria. Secretory proteins targeted to the Sec pathway by their N-terminal signal peptide bind to SecA, which couples binding and hydrolysis of adenosine triphosphate with movement of the secretory protein across the membrane-embedded SecYEG protein translocon. The phylogenetic diversity of bacteria raises the important question as to whether the region of SecA where the pre-protein binds has conserved sequence features that might impact the reaction mechanism of SecA. To address this question we established a large data set of SecA protein sequences and implemented a protocol to cluster and analyze these sequences according to features of two of the SecA functional domains, the protein binding domain and the nucleotide-binding domain 1. We identify remarkable sequence diversity of the protein binding domain, but also conserved motifs with potential role in protein binding. The N-terminus of SecA has sequence motifs that could help anchor SecA to the membrane. The overall sequence length and net estimated charge of SecA sequences depend on the organism.

Keywords

SecA
Clustering protocol
Phylogenetic information
Charge of SecA sequences
Lipid binding motif
NBD1 and PBD sequence clusters

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