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|General category ||Processes_IC|
|Detailed category ||Transport|
Document: Function annotation of SCOP domain superfamilies
UniProtKB KeyWords (KW)(show details)
Highlighted in gray are those with FDR_all>0.001
Document: KW annotation of SCOP domains
|Cross references ||IPR003708 SSF54611 Protein matches|
Secretion across the inner membrane in some Gram-negative bacteria occurs
via the preprotein translocase pathway. Proteins are produced in the
cytoplasm as precursors, and require a chaperone subunit to direct them to
the translocase component . From there, the mature proteins are either
targeted to the outer membrane, or remain as periplasmic proteins. The
translocase protein subunits are encoded on the bacterial chromosome.
The translocase itself comprises 7 proteins, including a chaperone protein
(SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and
SecG), and two additional membrane proteins that promote the release of
the mature peptide into the periplasm (SecD and SecF) . The chaperone
protein SecB  is a highly acidic homotetrameric protein that exists
as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains
preproteins in an unfolded state after translation, and targets these to
the peripheral membrane protein ATPase SecA for secretion .
Recently, the tertiary structure of Haemophilus influenzae SecB was resolved
by means of X-ray crystallography to 2.5A . The chaperone comprises four
chains, forming a tetramer, each chain of which has a simple alpha+beta fold
arrangement. While one binding site on the homotetramer recognises unfolded
polypeptides by hydrophobic interactions, the second binds to SecA through
the latter's C-terminal 22 residues.
PDBeMotif information about ligands, sequence and structure motifs
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Internal database links
Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry
out SCOP domain assignments to all genomes at the superfamily level.
Alignments of sequences to 5 models
in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical
are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.
Browse and view proteins in genomes which have
different domain combinations including a SecB-like domain.
Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.
Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.
There are 5 hidden Markov models representing the SecB-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.
Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · UniProtKB KeyWords (KW) · Internal database links ]