Structure-based working model of SecDF, a proton-driven bacterial protein translocation factor
Open accessAbstract
The bacterial membrane protein SecDF enhances protein translocation across the membrane driven by the complex of SecA ATPase and SecYEG. Many newly synthesized proteins in the cytoplasm are programmed to be translocated to the periplasm via the narrow channel that is formed in the center of SecYEG. During the protein-translocation process, SecDF is proposed to undergo repeated conformational transitions to pull out the precursor protein from the SecYEG channel into the periplasm. Once SecDF captures the precursor protein on the periplasmic surface, SecDF can complete protein translocation even if SecA function is inactivated by ATP depletion, implying that SecDF is a protein-translocation motor that works independent of SecA. Structural and functional analyses of SecDF in 2011 suggested that SecDF utilizes the proton gradient and interacts with precursor protein in the flexible periplasmic region. The crystal structures of SecDF in different states at more than 3Å resolution were reported in 2017 and 2018, which further improved our understanding of the dynamic molecular mechanisms of SecDF. This review summarizes recent structural studies of SecDF.
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Gene /0412 is a putative secDF protein export enhancing membrane component.
“we have further support to annotate /0412 as a putative secDF protein export enhancing membrane component.”
From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [81]
The CHARACTERIZATION OF SecDF section describes SecDF as a membrane-protein complex involved in protein translocation and reports reduced translocation efficiency when it is depleted. That supports the proposed function, but the paper does not identify gene /0412 or establish that it encodes SecDF. No page number is available in our copy. (LLM, conf=0.84)
Experimental — accuracy not yet measuredGene /0412 is secDF, a protein translocase subunit involved in cell membrane.
“secDF/0412 | cell membrane | protein translocase subunit”
From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [81]
The CHARACTERIZATION OF SecDF section (page unavailable) describes SecD and SecF as membrane proteins that form SecDF and participate in protein translocation. It does not identify the specific gene or locus /0412 as secDF. (LLM, conf=0.85)
Experimental — accuracy not yet measuredEach of the SecD and SecF regions contains conserved sequence motifs observed across a variety of organisms.
“Each of these two regions contains conserved sequence motifs that have been observed for both SecD and SecF across a variety of organisms,81 that previously supported the putative assignment of the analogous gene in M. florum L1 as secDF-like.34”
From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [81]
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Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell
Fu, E., Thornburg, Z. R., Brier, T. A., Wei, R., Yuan, B., Gilbert, B. R., Wang, S., & Luthey-Schulten, Z. A. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c04532 · Cited by 2 · see citing works
Substrate Proteins Take Shape at an Improved Bacterial Translocon
Oliver, D. B. (2018) · Journal of Bacteriology · doi:10.1128/jb.00618-18 · Cited by 2 · see citing works
Miyazaki, R., Kohga, H., 松岡, 奈., Maruno, Y., Yoshimoto, W., Takahashi, Y. S., Yanto, D. H. Y., Nugraha, Y., Shigematsu, H., Shiota, T., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-76843-3 · Cited by 1 · see citing works
Self-citationSecA-Mediated Protein Translocation through the SecYEG Channel
Komarudin, A. G., & Driessen, A. J. M. (2019) · ASM Press eBooks · doi:10.1128/9781683670285.ch2 · Cited by 1 · see citing works
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Strach, M., Koch, F., Fiedler, S. M., Liebeton, K., & Graumann, P. L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.09.507258
Bacterial Protein Transport Pathways and Analogous Conserved Pathways in Eukaryotes
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Self-citationStrach, M., Koch, F., Fiedler, S. M., Liebeton, K., & Graumann, P. L. (2023) · Figshare · doi:10.6084/m9.figshare.24248040
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Membrane Protein Insertion in Cells: Principles, Pathways, and Quality Control
Peled‐Zehavi, H., Yemini, R., & Fluman, N. (2026) · Chemical Reviews · doi:10.1021/acs.chemrev.5c01033
Structure and function of Salmonella inner membrane
Liu, X., Wang, Y., Sun, J., Guo, Z., Hu, A., Guo, J., J, J., Li, W., & Zhang, S. (2026) · Archives of Microbiology · doi:10.1007/s00203-026-05029-8
Crystal structure of YidC in complex with YibN
Takahashi, Y. S., Miyazaki, R., Kohga, H., & Tsukazaki, T. (2026) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2026.154668
Self-citation
- Authors
- Tsukazaki, T.
- Affiliations
- Nara Institute of Science and Technology (JP)
- Corresponding author
- Tsukazaki, Tomoya
- ORCID
- Tsukazaki, Tomoya
- Venue
- FEMS Microbiology Letters
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-04-27
- Volume
- 365
- Issue
- 12
- ISSN
- 0378-1097 (ISSN-L)
- 1574-6968
- PMC
- PMC5974789
- OpenAlex
- W2802451127
- Cited by
- 55
- References
- 55
- Citations by year
- 2026: 8 · 2025: 5 · 2024: 5 · 2023: 4 · 2022: 12 · 2021: 4 · 2020: 6 · 2019: 7 · 2018: 4
- FWCI
- 0.73
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- FEMS Microbiology Letters (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Institutional Repositories DataBase (IRDB) (submittedVersion)
- NAIST Digital Library (Nara Institute of Science and Technology) (submittedVersion, cc-by-nc-nd)
- Funders
- JSPS/MEXT KAKENHI (JP26119007, JP26291023, JP16K14713)
- Medical and Pharmaceutical Research, and PRESTO, JST (JPMJPR12L3)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Heat shock proteins research
- Keywords
- SecDF, protein translocation, SecYEG channel, SecA ATPase, conformational change, crystal structure, bacterial membrane proteins
- MeSH terms
- Amino Acid Sequence, Bacteria, Bacterial Proteins, Crystallization, Membrane Proteins, Protons, Crystallography, X-Ray, Protein Transport, Membrane Transport Proteins
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