Protein Family Models

This domain is found in Protein translocase subunit SecDF from Thermus thermophilus, which belongs to the RND superfamily. SecDF shows 12 transmembrane (TM) regions and 6 periplasmic regions (P1-P6). This entry represents the N-terminal region of the base subdomain of the P1 domain that is located in the N- terminal half of the polypeptide, also known as SecD region. This domain folds into a a pseudo-symmetrical anti-parallel beta-sheet that rearranges to a beta-barrel architecture during ion transport. This domain, which covers the TM region [1-4], is related to Pfam:PF03176 and usually appears associated with Pfam:PF07549 and Pfam:PF02355. Paper describing PDB structure 3aqo. [1]. 21562494. Structure and function of a membrane component SecDF that enhances protein export. Tsukazaki T, Mori H, Echizen Y, Ishitani R, Fukai S, Tanaka T, Perederina A, Vassylyev DG, Kohno T, Maturana AD, Ito K, Nureki O;. Nature. 2011;474:235-238. Paper describing PDB structure 5mg3. [2]. 27924919. A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion. Botte M, Zaccai NR, Nijeholt JL, Martin R, Knoops K, Papai G, Zou J, Deniaud A, Karuppasamy M, Jiang Q, Roy AS, Schulten K, Schultz P, Rappsilber J, Zaccai G, Berger I, Collinson I, Schaffitzel C;. Sci Rep. 2016;6:38399. Paper describing PDB structure 5xam. [3]. 28467902. Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF. Furukawa A, Yoshikaie K, Mori T, Mori H, Morimoto YV, Sugano Y, Iwaki S, Minamino T, Sugita Y, Tanaka Y, Tsukazaki T;. Cell Rep. 2017;19:895-901. [4]. 29398525. Remote Coupled Drast. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

This entry represents the head subdomain from P1 domain from SecDF proteins, which constitutes a critical element for proton transport [1-3]. P1 domain P1 binds an unfolded protein, and undergoes functionally important conformational changes. SecDF functions as a membrane-integrated chaperone that mediates ATP-independent protein translocation. Paper describing PDB structure 3aqo. [1]. 21562494. Structure and function of a membrane component SecDF that enhances protein export. Tsukazaki T, Mori H, Echizen Y, Ishitani R, Fukai S, Tanaka T, Perederina A, Vassylyev DG, Kohno T, Maturana AD, Ito K, Nureki O;. Nature. 2011;474:235-238. Paper describing PDB structure 5mg3. [2]. 27924919. A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion. Botte M, Zaccai NR, Nijeholt JL, Martin R, Knoops K, Papai G, Zou J, Deniaud A, Karuppasamy M, Jiang Q, Roy AS, Schulten K, Schultz P, Rappsilber J, Zaccai G, Berger I, Collinson I, Schaffitzel C;. Sci Rep. 2016;6:38399. Paper describing PDB structure 5xam. [3]. 28467902. Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF. Furukawa A, Yoshikaie K, Mori T, Mori H, Morimoto YV, Sugano Y, Iwaki S, Minamino T, Sugita Y, Tanaka Y, Tsukazaki T;. Cell Rep. 2017;19:895-901. (from Pfam)

Date:

2024-10-21

This domain appears to be the fist transmembrane region of the SecD export protein. SecD is directly involved in protein secretion and important for the release of proteins that have been translocated across the cytoplasmic membrane. [1]. 16452406. Archaeal and bacterial SecD and SecF homologs exhibit striking structural and functional conservation. Hand NJ, Klein R, Laskewitz A, Pohlschroder M;. J Bacteriol. 2006;188:1251-1259. [2]. 8428584. SecD is involved in the release of translocated secretory proteins from the cytoplasmic membrane of Escherichia coli. Matsuyama S, Fujita Y, Mizushima S;. EMBO J. 1993;12:265-270. (from Pfam)

Date:

2024-10-16

This family consists of various prokaryotic SecD and SecF protein export membrane proteins. This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC [1]. SecD and SecF are required to maintain a proton motive force [2]. This alignment encompasses a -GG- motif typically found in N-terminal half of the SecD/SecF proteins . [1]. 9694879. SecDF of Bacillus subtilis, a molecular Siamese twin required for the efficient secretion of proteins. Bolhuis A, Broekhuizen CP, Sorokin A, van Roosmalen ML, Venema G, Bron S, Quax WJ, van Dijl JM;. J Biol Chem 1998;273:21217-21224. [2]. 8112309. SecD and SecF are required for the proton electrochemical gradient stimulation of preprotein translocation. Arkowitz RA, Wickner W;. EMBO J 1994;13:954-963. (from Pfam)

Date:

2024-10-16

Members of this family are putative integral membrane proteins from bacteria. Several of the members are mycobacterial proteins. Many of the proteins contain two copies of this aligned region. The function of these proteins is not known, although it has been suggested that they may be involved in lipid transport [1]. [1]. 10694977. Analysis of the proteome of Mycobacterium tuberculosis in silico. Tekaia F, Gordon SV, Garnier T, Brosch R, Barrell BG, Cole ST;. Tuber Lung Dis 1999;79:329-342. (from Pfam)

Date:

2024-10-16

This family consists of various prokaryotic SecD and SecF protein export membrane proteins. This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC [1]. SecD and SecF are required to maintain a proton motive force [2]. [1]. 9694879. SecDF of Bacillus subtilis, a molecular Siamese twin required for the efficient secretion of proteins. Bolhuis A, Broekhuizen CP, Sorokin A, van Roosmalen ML, Venema G, Bron S, Quax WJ, van Dijl JM;. J Biol Chem 1998;273:21217-21224. [2]. 8112309. SecD and SecF are required for the proton electrochemical gradient stimulation of preprotein translocation. Arkowitz RA, Wickner W;. EMBO J 1994;13:954-963. (from Pfam)

Date:

2024-10-16

Members of this family are highly variable in length immediately after the well-conserved motif LGLGLXGG at the amino-terminal end of this model. Archaeal homologs are not included in the seed and score between the trusted and noise cutoffs. SecD from Mycobacterium tuberculosis has a long Pro-rich insert.

Gene:

secD

Date:

2024-06-04

protein translocase subunit SecD is part of the Sec protein translocase complex; interacts with the SecYEG preprotein conducting channel

Date:

2023-03-17

The SecA,SecB,SecD,SecE,SecF,SecG and SecY proteins form the protein translocation appartus in prokaryotes. This family is specific for the SecD and SecF proteins.

Date:

2019-09-10