Biomaterial Database

Structural insights into the secretin translocation channel in the type II secretion system. 2017

Zhaofeng Yan, and Meng Yin, and Dandan Xu, and Yongqun Zhu, and Xueming Li

School of Life Sciences, Tsinghua University, Beijing, China.

The secretin GspD of the type II secretion system (T2SS) forms a channel across the outer membrane in Gram-negative bacteria to transport substrates from the periplasm to the extracellular milieu. The lack of an atomic-resolution structure of the GspD channel hinders the investigation of substrate translocation mechanism of T2SS. Here we report cryo-EM structures of two GspD channels (∼1 MDa), from Escherichia coli K12 and Vibrio cholerae, at ∼3 Å resolution. The structures reveal a pentadecameric channel architecture, wherein three rings of GspD N domains form the periplasmic channel. The secretin domain constitutes a novel double β-barrel channel, with at least 60 β-strands in each barrel, and is stabilized by S domains. The outer membrane channel is sealed by β-strand-enriched gates. On the basis of the partially open state captured, we proposed a detailed gate-opening mechanism. Our structures provide a structural basis for understanding the secretin superfamily and the mechanism of substrate translocation in T2SS.

UI	MeSH Term	Description	Entries
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D004926	Escherichia coli	A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.	Alkalescens-Dispar Group,Bacillus coli,Bacterium coli,Bacterium coli commune,Diffusely Adherent Escherichia coli,E coli,EAggEC,Enteroaggregative Escherichia coli,Enterococcus coli,Diffusely Adherent E. coli,Enteroaggregative E. coli,Enteroinvasive E. coli,Enteroinvasive Escherichia coli
D000069178	Type II Secretion Systems	Gram-negative bacterial secretion systems which carry out the secretion of folded proteins.T2SSs secrete folded proteins from the PERIPLASMIC SPACE that have been exported there by SEC TRANSLOCASE or TAT SECRETION SYSTEMS, or they secrete folded proteins directly from the CYTOPLASM. The T2SSs have four substructures, an ATPase, an inner membrane platform, a pseudopilin, and secretin, an outer membrane complex which is a channel for secretion. (This bacterial secretin is not the same as the mammalian hormone also named SECRETIN.)	Bacterial Secretion System, Type II,T2SS Secretion System,Type 2 Secretion System,Type 2 Secretion Systems,Type II Secretion System,Secretion System, T2SS,System, T2SS Secretion
D000072757	Protein Conformation, beta-Strand	A secondary structure of proteins where the amino (N-H) groups of a polypeptide backbone, three to ten amino acids in length, establish hydrogen bonds with the carbonyl (C	Protein Conformation, beta-Sheet,beta-Pleated Sheet,beta-Sheet,beta-Sheets,beta-Strand,beta-Stranded Structures,beta-Strands,Conformation, beta-Sheet Protein,Conformation, beta-Strand Protein,Conformations, beta-Sheet Protein,Conformations, beta-Strand Protein,Protein Conformation, beta Sheet,Protein Conformation, beta Strand,Protein Conformations, beta-Sheet,Protein Conformations, beta-Strand,Sheet, beta-Pleated,Sheets, beta-Pleated,beta Pleated Sheet,beta Sheet,beta Sheets,beta Strand,beta Stranded Structures,beta Strands,beta-Pleated Sheets,beta-Sheet Protein Conformation,beta-Sheet Protein Conformations,beta-Strand Protein Conformation,beta-Strand Protein Conformations,beta-Stranded Structure
D000595	Amino Acid Sequence	The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.	Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D012633	Secretin	A peptide hormone of about 27 amino acids from the duodenal mucosa that activates pancreatic secretion and lowers the blood sugar level. (USAN and the USP Dictionary of Drug Names, 1994, p597)	Secrepan,Secretin Citrate, Pig,Secretin Maleate, Pig,Secretin Pentacetate, Pig,Secretin Sulfate, Pig,Secretin, Pig,Secretin-KABI,Pig Secretin,Pig Secretin Citrate,Pig Secretin Maleate,Pig Secretin Pentacetate,Pig Secretin Sulfate,Secretin KABI,SecretinKABI
D015640	Ion Channel Gating	The opening and closing of ion channels due to a stimulus. The stimulus can be a change in membrane potential (voltage-gated), drugs or chemical transmitters (ligand-gated), or a mechanical deformation. Gating is thought to involve conformational changes of the ion channel which alters selective permeability.	Gating, Ion Channel,Gatings, Ion Channel,Ion Channel Gatings
D017124	Conserved Sequence	A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.	Conserved Sequences,Sequence, Conserved,Sequences, Conserved
D054730	Protein Interaction Domains and Motifs	Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.	Protein Interaction Domains,Protein Interaction Motifs,Binding Motifs, Protein Interaction,Protein Interaction Binding Motifs,Protein-Protein Interaction Domains,Domain, Protein Interaction,Domain, Protein-Protein Interaction,Domains, Protein Interaction,Domains, Protein-Protein Interaction,Motif, Protein Interaction,Motifs, Protein Interaction,Protein Interaction Domain,Protein Interaction Motif,Protein Protein Interaction Domains,Protein-Protein Interaction Domain
D018272	Porins	Porins are protein molecules that were originally found in the outer membrane of GRAM-NEGATIVE BACTERIA and that form multi-meric channels for the passive DIFFUSION of WATER; IONS; or other small molecules. Porins are present in bacterial CELL WALLS, as well as in plant, fungal, mammalian and other vertebrate CELL MEMBRANES and MITOCHONDRIAL MEMBRANES.	Pore Protein,Pore Proteins,Porin,Protein, Pore,Proteins, Pore