TCDB is operated by the Saier Lab Bioinformatics Group
TCIDNameDomainKingdom/PhylumProtein(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