TCID | Name | Domain | Kingdom/Phylum | Protein(s) |
---|---|---|---|---|
9.B.104.1.1 | GlpG rhomboid serine protease (276aas ; 6 TMSs; DUF3582; Structure known) (Vinothkumar, 2011; Wang et al. 2006). The requirements for cleavage have been defined (Akiyama and Maegawa 2007). The catalytic Ser201, is located at the N terminus of TMS 4, approximately 10 Å below the membrane surface. Access to water molecules is provided by a central cavity that opens to the extracellular region and converges on Ser201. One of the two GlpG molecules in the asymmetric unit has an open conformation at the active site, with TMS 5 bent away from the rest of the molecule. Substrate entry to the active site is probably gated by the movement of TMS 5 (Wu et al. 2006). Rhomboid proteases GlpG and Rhom7 are involved in membrane protein quality control by specifically targeting components of respiratory complexes. The metastable transmembrane domains of rhomboid substrates are protected when they are incorporated into a functional complex (Liu et al. 2020). | Bacteria |
Pseudomonadota | GlpG of E. coli (P09391) |
9.B.104.1.2 | Rhomboid (S54) superfamily protein (RSP) | Archaea |
Euryarchaeota | RSP of Methanosarcina barkeri (Q46G03) |
9.B.104.1.3 | Putative transporter (223 aas; 6 TMSs). Predicted peptidase S54, rhomboid. | Bacteria |
Bacillota | Putative transporter of Clostridium sp.D5 (F0Z2G1) |
9.B.104.1.4 | Serine protease, rhomboid (PSS4 peptidase family), of 625 aas and 7 TMSs.. | Bacteria |
Pseudomonadota | Rhomboid of E. coli |
9.B.104.1.5 | Rhomboid protease homologue | Bacteria |
Spirochaetota | Rhomboid homologue of Leptospira interrogans (Q8F2A9) |
9.B.104.1.6 | Mitochondrial PARL rhomboid protease of 379 aas. Required for the control of apoptosis during postnatal growth. Essential for proteolytic processing of an antiapoptotic form of OPA1 which prevents the release of mitochondrial cytochrome c in response to intrinsic apoptoptic signals. Impaired in Parkinson Disease (Meissner et al. 2015). | Eukaryota |
Metazoa, Chordata | PARL of Homo sapiens |
9.B.104.1.7 | Rhomboid protease (peptidase) of 192 aas and 6 TMSs, GlpG. The structure has been solved at 2.2 Å resolution, revealing the relative disposition of the nucleophilic serine to the general base/acid function of the conserved histidine (Lemieux et al. 2007). The active site is inside the membrane, but near the surface, to release the hydrophilic ectodomain of its single TMS substrate. These enzymes may thin the membrane, allowing access of water to the active site. There is a cavity adjacent to the cleavage site containing ordered water molecules, involved in access to the substrate before cleavage (Sanders and Hutchison 2018). Factors that control the force needed to unfold a membrane protein in silico depend on the mode of denaturation (Faruk et al. 2023). | Bacteria |
Pseudomonadota | GlpG of Haemophilus influenzae |
9.B.104.1.8 | Rhomboid family intramembrane serine protease of 268 aas and 6 TM | Archaea |
Euryarchaeota | Rhomboid of Candidatus Methanoperedens nitroreducens |
9.B.104.1.9 | GlpG-like rhomboid protease (C-terminal) with an N-terminal Zinc finger AN1-like domain, of 321 aas with 6 - 8 TMSs. | Archaea |
Candidatus Lokiarchaeota | Rhomboid protease of Lokiarchaeum sp. |
9.B.104.1.10 | Rhomboid family intramembrane serine proteaseof 241 aas and 6 TMSs. | Bacteria |
Bacteroidota | Rhomboid protease of Mucilaginibacter kameinonensis |
9.B.104.1.11 | Putative rhomboid protease of 858 aas and 6 C-terminal TMSs (Nakagawa et al. 2005). | Eukaryota |
Metazoa, Chordata | Rhomboid protease of Cynoglossus semilaevis |
9.B.104.1.12 | Uncharacterized inactive rhomboid protein 1-like isoform X. The last TMSs may be distantly related to the 9.B.306 CaBP family members which are thought to bind calcium ions. | Eukaryota |
Metazoa, Chordata | UP of Sinocyclocheilus grahami |
9.B.104.2.1 | Rhomboid protease (355 aas; 7TMSs) | Eukaryota |
Metazoa, Arthropoda | Rhomboid of Drosophila melanogaster (P20350) |
9.B.104.3.1 | Rhomboid family protein | Bacteria |
Cyanobacteriota | Rhomboid protein of Prochlorococcus marinus |
9.B.104.3.2 | Rhomboid family protein | Bacteria |
Bacteroidota | Rhomboid protein of Bacteriodes fragilis |
9.B.104.3.3 | Rhomboid family protein | Bacteria |
Actinomycetota | Rhomboid protein of Corynebacterium glutamicum |
9.B.104.3.4 | Rhomboid protease of 233 aas | Bacteria |
Bdellovibrionota | Protease of Bdellovibrio exovorus |
9.B.104.4.1 | The rhomboid-related protein 4, RHBDL4 (Fleig et al. 2012). | Eukaryota |
Metazoa, Chordata | RHBDL4 of Homo sapiens (Q8TEB9) |
9.B.104.4.2 | RHOMBOID-like protein 13 of 269 aas and 7 TMSs | Eukaryota |
Viridiplantae, Streptophyta | Rhomboid protein of Hevea brasiliensis |
9.B.104.4.3 | Rhomboid-like protein 15, isoform X2of 407 aas and 6 N-terminal TMSs. | Eukaryota |
Viridiplantae, Streptophyta | Rhomboid protein of Raphanus sativus |
9.B.104.4.4 | Rhomboid domain-containing protein 2, RHBDD2, of 364 aas and 5 or 6 TMSs. | Eukaryota |
Metazoa, Chordata | RHBDD2 of Homo sapiens |
9.B.104.5.1 | Putative rhomboid protein | Bacteria |
Planctomycetota | Rhomboid of Rhodopirellula baltica |
9.B.104.5.2 | Rhombosortase of 275 aas and 6 TM | Bacteria |
Planctomycetota | Rhomboid of Roseimaritima ulvae |
9.B.104.5.3 | Rhombosortase of 197 aas and 6 TM | Bacteria |
Pseudomonadota | Rhombosortase of Candidatus Thiodiazotropha endolucinida |
9.B.104.6.1 | 7 TMS rhomboid family protein; shows sequence similarity to members of the MFS. Also homologous to the DUF1751 family. | Bacteria |
Myxococcota | 7 TMS rhomboid family protein of Myxococcus xanthus |
9.B.104.6.2 | Rhomboid family proteinof 275 aas and 5 - 6 TMSs. | Bacteria |
Myxococcota | Rhomboid of Labilithrix luteola |
9.B.104.6.3 | Rhomboid family intramembrane serine proteaseof 245 aas and 6 TM | Bacteria |
Myxococcota | Rhomboid of Vulgatibacter incomptus |
9.B.104.7.1 | Rhomboid protease | Bacteria |
Bacillota | Rhomboid protease of Lactobacillus rhamnosus |