Summary: Cytoplasmic N-terminal domain of rhomboid serine protease
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Cytoplasmic N-terminal domain of rhomboid serine protease Provide feedback
Rhomboid_N is the N-terminal cytoplasmic domain of the rhomboid intra-membraneous serine protease, otherwise known as Peptidase_S54, PF01694. This N-terminal domain has similarity to other GlnB-like domains, some of which appear to have a binding role, eg to peptidoglycan. It is not clear exactly what the function of this domain is in the protease, but its presence is critical for maintaining a catalytically competent state for the protein .
Sherratt AR, Blais DR, Ghasriani H, Pezacki JP, Goto NK;, Biochemistry. 2012;51:7794-7803.: Activity-based protein profiling of the Escherichia coli GlpG rhomboid protein delineates the catalytic core. PUBMED:22963263 EPMC:22963263
Internal database links
|Similarity to PfamA using HHSearch:||NRho|
This tab holds annotation information from the InterPro database.
InterPro entry IPR022732
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [PUBMED:7845208]. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence [PUBMED:7845208]. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases [PUBMED:7845208].
Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base [PUBMED:7845208]. The geometric orientations of the catalytic residues are similar between families, despite different protein folds [PUBMED:7845208]. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [PUBMED:7845208, PUBMED:8439290].
This entry represents the N-terminal domain of membrane-bound serine endopeptidases belonging to MEROPS peptidase family S54 (rhomboid-1, clan ST). This domain contains a conserved ASW sequence motif and a single completely conserved residue F that may be functionally important.
The tertiary structure of the GlpG protein from Escherichia coli has been determined [PUBMED:1705116]. The GlpG protein has six transmembrane domains (other members of the family are predicted to have seven), with the N- and C-terminal ends anchored in the cytoplasm. One transmembrane domain is shorter than the rest, creating an internal, aqueous cavity just below the membrane surface and it is here were proteolysis occurs. There is also a membrane-embedded loop between the first and second transmembrane domains which is postulated to act as a gate controlling substrate access to the active site. No other family of serine peptidases is known to have active site residues within transmembrane domains (although transmembrane active sites are known for aspartic peptidase and metallopeptidases), and the GlpG protein has the type structure for clan ST.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||integral component of membrane (GO:0016021)|
|Molecular function||serine-type endopeptidase activity (GO:0004252)|
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The members of this clan are characterised by the fact the domains, each comprised of four beta-strand and two alpha helices, tend to form tetrameric structures .
The clan contains the following 12 members:Amidase02_C CdAMP_rec CutA1 DUF190 DUF2007 DUF2179 DUF3240 HisG_C Nit_Regul_Hom NRho P-II Rhomboid_N
We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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Curation and family details
|Seed source:||PFAM-B_2087 (release 23.0), pdb:2lep|
|Author:||Assefa S, Bateman A|
|Number in seed:||22|
|Number in full:||222|
|Average length of the domain:||84.60 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||30.23 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Rhomboid_N domain has been found. There are 4 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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