Crystallization and preliminary X-ray diffraction of the first periplasmic domain of SecDF, a translocon-associated membrane protein, from<i>Thermus thermophilus</i>

Echizen, Yuka; Tsukazaki, Tomoya; Dohmae, Naoshi; Ishitani, Ryuichiro; Nureki, Osamu

doi:10.1107/s1744309111031885

Cited by 5 publications

(3 citation statements)

References 19 publications

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“…Besides its direct role in protein translocation, as mentioned, SecDF is also required for the maintenance of proton motive force levels, which are needed for efficient translocation (13,15). It is due to these and related functions that the lack of SecDF results in severe growth retardation and defects in protein export in vivo (16,17). Moreover, its important role in the translocation of several virulence factors, and hence in the bacterial infection process, makes SecDF an important possible drug target for preventing bacterial infections.…”

Section: Introductionmentioning

confidence: 99%

Electric-Field-Induced Protein Translocation via a Conformational Transition in SecDF: An MD Study

Ficici

Jeong

Andricioaei

2017

Biophysical Journal

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SecDF is an important component of the Sec protein translocation machinery embedded in the bacterial membrane, which is associated with many functions, such as stabilizing other Sec translocon components within the membrane, maintaining the transmembrane (TM) potential, and facilitating the ATP-independent stage of the translocation mechanism. Related studies suggest that SecDF undergoes functionally important conformational changes that involve mainly its P1-head domain and that these changes are coupled with the proton motive force (Δp). However, there still is not a clear understanding of how SecDF functions, its exact role in the translocation machinery, and how its function is related to Δp. Here, using all-atom molecular dynamics simulations combined with umbrella sampling, we study the P1-head conformational change and how it is coupled to the proton motive force. We report potentials of mean force along a root-mean-square-distance-based reaction coordinate obtained in the presence and absence of the TM electrical potential. Our results show that the interaction of the P1 domain dipole moment with the TM electrical field considerably lowers the free-energy barrier in the direction of F-form to I-form transition.

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Section: Introductionmentioning

confidence: 99%

Electric-Field-Induced Protein Translocation via a Conformational Transition in SecDF: An MD Study

Ficici

Jeong

Andricioaei

2017

Biophysical Journal

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“…The head and base subdomains are connected by two linkers that might act as hinges. The segment of the P1 domain extending from residue number 36 to 263 has also been crystallized [6,7]. Notably, the conformation of P1 in this 2.6 Å structure differs from that in full-length wild type (wt) TSecDF.…”

Section: Introductionmentioning

confidence: 99%

Conformational variation of the translocon enhancing chaperone SecDF

Mio

Tsukazaki

Mori

et al. 2013

J Struct Funct Genomics

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The Sec translocon facilitates transportation of newly synthesized polypeptides from the cytoplasm to the lumen/periplasm across the phospholipid membrane. Although the polypeptide-conducting machinery is formed by the SecYEG-SecA complex in bacteria, its transportation efficiency is markedly enhanced by SecDF. A previous study suggested that SecDF assumes at least two conformations differing by a 120° rotation in the spatial orientation of the P1 head subdomain to the rigid base, and that the conformational dynamics plays a critical role in polypeptide translocation. Here we addressed this hypothesis by analyzing the 3D structure of SecDF using electron tomography and single particle reconstruction. Reconstruction of wt SecDF showed two major conformations; one resembles the crystal structure of full-length SecDF (F-form structure), while the other is similar to the hypothetical structural variant based on the crystal structure of the isolated P1 domain (I-form structure). The transmembrane domain of the I-form structure has a scissor like cleft open to the periplasmic side. We also report the structure of a double cysteine mutant designed to constrain SecDF to the I-form. This reconstruction has a protrusion at the periplasmic end that nicely fits the orientation of P1 in the I-from. These results provide firm evidence for the occurrence of the I-form in solution and support the proposed F- to I-transition of wt SecDF during polypeptide translocation.

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“…Although the protein translocation is enhanced by the PMF 8 – 10 and SecDF 11 – 17 , the structure and role of SecDF have remained unclear. In this review, we describe the first 3D structure of SecDF and propose a new working model of the PMF-driven protein translocation by SecDF, based on its structural features and subsequent functional analyses 18 – 20 .…”

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confidence: 99%

The mechanism of protein export enhancement by the SecDF membrane component

Tsukazaki

Nureki

2011

BIOPHYSICS

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Protein transport across membranes is a fundamental and essential cellular activity in all organisms. In bacteria, protein export across the cytoplasmic membrane, driven by dynamic interplays between the protein-conducting SecYEG channel (Sec translocon) and the SecA ATPase, is enhanced by the proton motive force (PMF) and a membrane-integrated Sec component, SecDF. However, the structure and function of SecDF have remained unclear. We solved the first crystal structure of SecDF, consisting of a pseudo-symmetrical 12-helix transmembrane domain and two protruding periplasmic domains. Based on the structural features, we proposed that SecDF functions as a membrane-integrated chaperone, which drives protein movement without using the major energetic currency, ATP, but with remarkable cycles of conformational changes, powered by the proton gradient across the membrane. By a series of biochemical and biophysical approaches, several functionally important residues in the transmembrane region have been identified and our model of the SecDF function has been verified.

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Crystallization and preliminary X-ray diffraction of the first periplasmic domain of SecDF, a translocon-associated membrane protein, fromThermus thermophilus

Cited by 5 publications

References 19 publications

Electric-Field-Induced Protein Translocation via a Conformational Transition in SecDF: An MD Study

Electric-Field-Induced Protein Translocation via a Conformational Transition in SecDF: An MD Study

Conformational variation of the translocon enhancing chaperone SecDF

The mechanism of protein export enhancement by the SecDF membrane component

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