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27  structures 17410  species 3  interactions 29346  sequences 112  architectures

Family: Rhomboid (PF01694)

Summary: Rhomboid family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Rhomboid protease". More...

Rhomboid protease Edit Wikipedia article

Rhomboid
Identifiers
Symbol Rhomboid
Pfam PF01694
Pfam clan CL0207
InterPro IPR002610
MEROPS S54
SCOP 144092
SUPERFAMILY 144092
OPM superfamily 186
OPM protein 2ic8

The rhomboid proteases are a family of enzymes that exist in almost all species. They are proteases: they cut the polypeptide chain of other proteins. This proteolytic cleavage is irreversible in cells, and an important type of cellular regulation. Although proteases are one of the earliest and best studied class of enzyme, rhomboids belong to a much more recently discovered type: the intramembrane proteases. What is unique about intramembrane proteases is that their active sites are buried in the lipid bilayer of cell membranes, and they cleave other transmembrane proteins within their transmembrane domains.[1] About 30% of all proteins have transmembrane domains, and their regulated processing often has major biological consequences. Accordingly, rhomboids regulate many important cellular processes, and may be involved in a wide range of human diseases.

Intramembrane proteases

Rhomboids are intramembrane serine proteases.[2][3][4] The other types of intramembrane protease are aspartyl- and metallo-proteases, respectively. The presenilins and signal peptide peptidase-like family, which are intramembrane aspartyl proteases, cleave substrates that include the Notch receptor and the amyloid precursor protein, which is implicated in Alzheimer's disease. The site-2 protease family, which are intramembrane metalloproteases, regulate among other things cholesterol biosynthesis and stress responses in bacteria. The different intramembrane protease families are evolutionarily and mechanistically unrelated, but there are clear common functional themes that link them. Rhomboids are perhaps the best characterised class.

History of rhomboid discovery

Rhomboids were first named after a mutation in the fruitfly Drosophila, discovered in a famous genetic screen that led to a Nobel Prize for Christiane Nüsslein-Volhard and Eric Wieschaus.[5] In that screen they found a number of mutants with similar phenotypes: ‘pointy’ embryonic head skeletons. They named them each with a pointy-themed name – one was rhomboid. Genetic analysis later proved that this group of genes were members of the epidermal growth factor (EGF) receptor signalling pathway,[6][7] and that rhomboid was needed to generate the signal that activates the EGF receptor.[8][9] The molecular function of rhomboid took a bit longer to unravel but a combination of genetics and molecular techniques led to the discovery that Drosophila rhomboid and other members of the family were the first known intramembrane serine proteases.[2]

Biological role of rhomboids

Rhomboids were first discovered as proteases that regulate EGF receptor signalling in Drosophila. By releasing the extracellular domain of the growth factor Spitz, from its transmembrane precursor, rhomboid triggers signalling.[2][10] Since then, many other important biological functions have been proposed.[11][12]

Structure and enzyme function of rhomboids

Fig. 2: Crystal structure of the rhomboid-substrate peptide (P4-P1) complex and possible interaction modes of substrate transmembrane domain with rhomboid
(A) Crystal structure and molecular dynamics based model of the P4-P3' segment of a substrate bound in the active site of rhomboid as a Michaelis complex. The substrate exits the active site of GlpG by it P3' residue threading between W236 and F153. (B) Extended model of the full transmembrane substrate interacting with GlpG based on an NMR structure of E.coli TatA and homology modelling. The N-terminus of the helical transmembrane domain of the substrate continues from where the P3' residue exits the active site of GlpG. This arrangement suggests three principally different orientations of substrate TMD (shown in different colours).

Rhomboids were the first intramembrane proteases for which a high resolution crystal structure was solved.[33][34][35][36][37] These structures confirmed predictions that rhomboids have a core of six transmembrane domains, and that the catalytic site depends on a serine and histidine catalytic dyad. The structures also explained how a proteolytic reaction, which requires water molecules, can occur in the hydrophobic environment of a lipid bilayer: one of the central mysteries of intramembrane proteases.[38] The active site of rhomboid protease is in a hydrophilic indentation, in principle accessible to water from the bulk solution.[33][34][35][36][37] However, it has been proposed that there might be an auxiliary mechanism to facilitate access of water molecules to the catalytic dyad at the bottom of the active site to ensure catalytic efficiency.[39]

The active site of rhomboid protease is protected laterally from the lipid bilayer by its six constituent transmembrane helices, suggesting that substrate access to rhomboid active site is regulated. One area of uncertainty has been the route of substrate access. Substrates were initially proposed to enter between transmembrane domains (TMDs) 1 and 3,[33][36] but current evidence strongly supports an alternative access point, between TMDs 2 and 5.[34][35][37][40][41] This notion is also supported by the fact that mutations in TMD5 have only a marginal effect on the thermodynamic stability of rhomboid, unlike other regions of the molecule.[42] Very recently, the first ever co-crystal structure of an intramembrane protease - the E.coli rhomboid protease GlpG - and a substrate-derived peptide bound in the active site [43] confirms and extends this substrate access model and provides implications for the mechanism of other rhomboid-superfamily proteins.[44] The details of how a substrate TMD may be recognised by rhomboid are however still unclear. Some authors propose that substrate access involves a large lateral displacement movement of TMD5 to open up the core of rhomboid.[34][40] Other reports instead suggest that large lateral movement of TMD5 is not required,[45] and propose that the surface of TMDs 2 and 5 rather serves as an "intramembrane exosite" mediating the recognition of substrate TMD.[43][46]

Rhomboid specificity

Rhomboids do not cleave all transmembrane domains. In fact, they are highly specific, with a limited number of substrates. Most natural Rhomboid substrates known so far are type 1 single transmembrane domain proteins, with their amino termini in the luminal/extracellular compartment. However, recent studies suggested that type 2 membrane protein (i.e. with opposite topology: the amino terminus is cytoplasmic),[47] or even multipass membrane proteins could act as rhomboid substrates.[48] The specificity of rhomboids underlies their ability to control functions in a wide range of biological processes and, in turn, understanding what makes a particular transmembrane domain into a rhomboid substrate can shed light on rhomboid function in different contexts.

Initial work indicated that rhomboids recognise instability of the transmembrane alpha-helix at the site of cleavage as the main substrate determinant.[25][49] More recently, it has been found that rhomboid substrates are defined by two separable elements: the transmembrane domain and a primary sequence motif in or immediately adjacent to it.[46] This recognition motif directs where the substrate is cleaved, which can occur either within the transmembrane domain or just outside of it, in the juxtamembrane region.[46] In the former case helix destabilising residues downstream in substrate TMD are also necessary for efficient cleavage.[46] A detailed enzyme kinetics analysis has in fact shown that the recognition motif interactions with rhomboid active site determine the kcat of substrate cleavage.[50] The principles of substrate TMD recognition by rhomboid remain poorly understood, but numerous lines of evidence indicate that rhomboids (and perhaps also other intramembrane proteases) somehow recognise the structural flexibility or dynamics of transmembrane domain of their substrates.[39][51] Full appreciation of the biophysical and structural principles involved will require structural characterisation of the complex of rhomboid with the full transmembrane substrate.[52] As a first step towards this goal, a recent co-crystal structure of the enzyme in complex with a substrate-derived peptide containing mechanism-based inhibitor explains the observed recognition motif sequence preferences in rhomboid substrates structurally, and provides a significant advance in the current understanding of rhomboid specificity and mechanism of rhomboid-family proteins.[43]

In some Gram-negative bacteria, including Shewanella and Vibrio, up to thirteen proteins are found with GlyGly-CTERM, a C-terminal homology domain consisting of a glycine-rich motif, a highly hydrophobic transmembrane helix, and a cluster of basic residues. This domain appears to be the recognition sequence for rhombosortase, a branch of the rhomboid protease family limited to just those bacteria with the GlyGly-CTERM domain.[53]

Medical significance of rhomboids

The diversity of biological functions already known to depend on rhomboids is reflected in evidence that rhomboids play a role in a variety if diseases including cancer, parasite infection, and diabetes.[11][12] It is important to note, however, that there is no case yet established where a precise medical significance is fully validated.

No drugs that modulate rhomboid activity have yet been reported, although a recent study has identified small molecule, mechanism-based inhibitors that could provide a basis for future drug development.[54]

The rhomboid-like family

Rhomboid proteases appear to be conserved in all eukaryotes and the vast majority of prokaryotes. Bioinformatic analysis highlights that some members of the rhomboid family lack the amino acid residues essential for proteolysis, implying that they cannot cleave substrates. These ‘pseudoproteases’ include a subfamily that have been named the iRhoms [55] (also known as RHBDF1 and RHBDF2). iRhoms can promote the ER associated degradation (ERAD) of EGF receptor ligands in Drosophila, thus providing a mechanism for regulating EGF receptor activity in the brain.[56] This implies that the fundamental cellular quality control mechanism is exploited by multicellular organisms to regulate signalling between cells. Interestingly, in the mouse, iRhoms are key trafficking chaperones required for the ER export of ADAM17/TACE and its maturation. iRhoms are thus required for the TNF-alpha and EGF receptor signalling, making them medically highly attractive.[56][57][58][59][60]

Phylogenetic analysis indicates that rhomboids are in fact members of a larger rhomboid-like superfamily or clan, which includes the derlin proteins, also involved in ERAD.[61]

References

  1. ^ Brown, M. S., Ye, J., Rawson, R. B. & Goldstein, J. L. Cell 100, 391-38. (2000)
  2. ^ a b c S. Urban, J. R. Lee, M. Freeman, Cell 107, 173 (2001)
  3. ^ Lemberg, M. K. et al. EMBO J. 24, 464-472 (2005
  4. ^ Urban, S. & Wolfe, M. S. Proc. Natl. Acad. Sci. U S A 102, 1883-1888 (2005)
  5. ^ G. Jürgens, E. Wieschaus, C. Nüsslein-Volhard, H. Kluding, Wilhelm Roux’s Arch. Dev. Biol. 193, 283 (1984)
  6. ^ M. A. Sturtevant, M. Roark, E. Bier, Genes Dev. 7, 961 (1993)
  7. ^ M. Freeman, Mech Dev 48, 25 (1994)
  8. ^ J. D. Wasserman, S. Urban, M. Freeman, Genes Dev. 14, 1651 (2000)
  9. ^ A. G. Bang, C. Kintner, Genes Dev. 14, 177 (2000)
  10. ^ J. R. Lee, S. Urban, C. F. Garvey, M. Freeman, Cell 107, 161 (2001)
  11. ^ a b M. Freeman, Annu. Rev. Genet. 42, 191 (2008)
  12. ^ a b S. Urban, Nat Rev Microbiol (2009)
  13. ^ C. Adrain, K. Strisovsky, M. Zettl, L. Hu, M. Lemberg, M. Freeman, EMBO Rep. 12, 421 (2011)
  14. ^ J. C. Pascall, K. D. Brown, Biochem. Biophys. Res. Commun. 317, 244 (2004)
  15. ^ O. Lohi, S. Urban, M. Freeman, Curr. Biol. 14, 236 (2004)
  16. ^ T.L. Cheng, Y.T. Wu, H.Y. Lin, F.C. Hsu, S.K. Liu, B.I. Chang, W.S. Chen, C.H. Lai, G.Y. Shi, H.L. Wu, J. Invest. Dermatol. 131, 2486-2494 (2011)
  17. ^ M. Herlan, F. Vogel, C. Bornhovd, W. Neupert, A. S. Reichert, J. Biol. Chem. 278, 27781 (2003)
  18. ^ G. A. McQuibban, S. Saurya, M. Freeman, Nature 423, 537 (2003)
  19. ^ G. A. McQuibban, J. R. Lee, L. Zheng, M. Juusola, M. Freeman, Curr. Biol. 16, 982 (2006)
  20. ^ a b S. Cipolat et al., Cell 126, 163 (2006)
  21. ^ A. E. Civitarese et al., Cell Metab 11, 412 (2010).
  22. ^ A. J. Whitworth et al., Dis Model Mech 1, 168 (2008)
  23. ^ E. Deas et al., Hum. Mol. Genet. 20, 867 (2011)
  24. ^ C. Meissner, H. Lorenz, A. Weihofen, D. J. Selkoe, M. K. Lemberg, J. Neurochem. 117, 856 (2011)
  25. ^ a b S. Urban, M. Freeman, Mol. Cell. 11, 1425 (2003)
  26. ^ R. P. Baker, R. Wijetilaka, S. Urban, PLoS Pathog. 2, e113 (2006)
  27. ^ R. A. O'Donnell et al., J. Cell Biol. 174, 1023 (2006)
  28. ^ J. M. Santos, D. J. Ferguson, M. J. Blackman, D. Soldati-Favre, Science 331, 473 (2011)
  29. ^ P. Srinivasan, . Coppens, M. Jacobs-Lorena, PLoS Pathog. 5: e1000262 (2009)
  30. ^ J.W. Lin, P. Meireles, M. Prudencio, et al., Mol. Microbiol. 88, 318-338 (2013)
  31. ^ L. A. Baxt, R. P. Baker, U. Singh, S. Urban, Genes Dev. 22, 1636 (2008)
  32. ^ L. G. Stevenson, K. Strisovsky, K. M. Clemmer, S. Bhatt, M. Freeman, P. N. Rather, Proc. Natl. Acad. Sci. U S A 104, 1003 (2007)
  33. ^ a b c Y. Wang, Y. Zhang, Y. Ha, Nature 444, 179 (2006)
  34. ^ a b c d Z. Wu et al., Nat Struct Mol Biol 13, 1084 (2006)
  35. ^ a b c A. Ben-Shem, D. Fass, E. Bibi, Proc. Natl. Acad. Sci. U S A 104, 462 (2007)
  36. ^ a b c M. J. Lemieux, S. J. Fischer, M. M. Cherney, K. S. Bateman, M. N. James, Proc. Natl. Acad. Sci. U S A 104, 750 (2007)
  37. ^ a b c K. R. Vinothkumar, J. Mol. Biol. 407, 232 (2011)
  38. ^ M. K. Lemberg, M. Freeman, Mol. Cell. 28, 930 (2007)
  39. ^ a b S.M. Moin, S. Urban, elife 1, e00173 (2012)
  40. ^ a b R. P. Baker, K. Young, L. Feng, Y. Shi, S. Urban, Proc. Natl. Acad. Sci. U S A 104, 8257 (2007)
  41. ^ Y. Wang, S. Maegawa, Y. Akiyama, Y. Ha, J. Mol. Biol. 374, 1104 (2007)
  42. ^ R.P. Baker, S. Urban, Nat. Chem. Biol. 8, 759-768 (2012)
  43. ^ a b c S. Zoll, S. Stanchev, J. Began, J. Skerle, M. Lepsik, L. Peclinovska, P. Majer, K. Strisovsky, EMBO J. 33, 2408-2421 (2014)
  44. ^ M. Freeman, Annu. Rev. Cell Dev. Biol. 30, 235-254 (2014)
  45. ^ Y. Xue, Y. Ha, J. Biol. Chem. 288, 16645-16654 (2013)
  46. ^ a b c d K. Strisovsky, H. J. Sharpe, M. Freeman, Mol. Cell. 36, 1048 (2009)
  47. ^ R. Tsruya et al., EMBO J. 26, 1211 (2007)
  48. ^ L. Fleig, N. Bergbold, P. Sahasrabudhe, B. Geiger, L. Kaltak, M. K. Lemberg, Mol. Cell 47, 558-569 (2012)
  49. ^ Y. Akiyama, S. Maegawa, Mol. Microbiol. 64, 1028 (2007)
  50. ^ S.W. Dickey, R.P. Baker, S. Cho, S. Urban, Cell 155, 1270-1281 (2013)
  51. ^ D. Langosch, C. Scharnagl, H. Steiner, M. K. Lemberg, Trends Biochem. Sci. 40, 318-327 (2015)
  52. ^ K. Strisovsky, FEBS J. 280, 1579-1603 (2013)
  53. ^ D. H. Haft and N. Varghese, PLoS One 6, e28886 (2011)
  54. ^ O. Pierrat, K. Strisovsky et al., ACS Chem Biol (2010)
  55. ^ M. K. Lemberg, M. Freeman, Genome Res. 17, 1634 (2007)
  56. ^ a b M. Zettl, C. Adrain, K. Strisovsky, V. Lastun, M. Freeman, Cell 145, 79 (2011)
  57. ^ C. Adrain, M. Zettl, Y. Christova, N. Taylor, M. Freeman, Science 335, 225-228 (2012)
  58. ^ D.R. McIlwain, P.A. Lang, T. Maretzky, K. Hamada, K. Ohishi, S.K. Maney, T. Berger, A. Murthy, G. Duncan, H.C. Xu, et al. Science 335, 229-232 (2012)
  59. ^ Y. Christova, C. Adrain, P. Bambrough, A. Ibrahim, M. Freeman, EMBO Rep. 14, 884-890 (2013)
  60. ^ X. Li, T. Maretzky, G. Weskamp, S. Monette, X. Qing, P.D. Issuree, H.C. Crawford, D.R. McIlwain, T.W. Mak, J.E. Salmon, et al. Proc. Natl. Acad. Sci. U. S. A. 112, 6080-6085 (2015)
  61. ^ http://pfam.sanger.ac.uk/clan/rhomboid-like

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Rhomboid family Provide feedback

This family contains integral membrane proteins that are related to Drosophila rhomboid protein P20350. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease [2] ( EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite [5].

Literature references

  1. Bier E, Jan LY, Jan YN; , Genes Dev 1990;4:190-203.: rhomboid, a gene required for dorsoventral axis establishment and peripheral nervous system development in Drosophila melanogaster. PUBMED:2110920 EPMC:2110920

  2. Urban S, Lee JR, Freeman M; , Cell 2001;107:173-182.: Drosophila rhomboid-1 defines a family of putative intramembrane serine proteases. PUBMED:11672525 EPMC:11672525

  3. Koonin EV, Makarova KS, Rogozin IB, Davidovic L, Letellier MC, Pellegrini L; , Genome Biol 2003;4:R19.: The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers. PUBMED:12620104 EPMC:12620104

  4. Urban S, Wolfe MS; , Proc Natl Acad Sci U S A. 2005;102:1883-1888.: Reconstitution of intramembrane proteolysis in vitro reveals that pure rhomboid is sufficient for catalysis and specificity. PUBMED:15684070 EPMC:15684070

  5. Brossier F, Jewett TJ, Sibley LD, Urban S; , Proc Natl Acad Sci U S A. 2005;102:4146-4151.: A spatially localized rhomboid protease cleaves cell surface adhesins essential for invasion by Toxoplasma. PUBMED:15753289 EPMC:15753289


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022764

This entry represents a six transmembrane helix rhomboid domain.

This domain is found in serine peptidases belonging to the MEROPS peptidase family S54 (Rhomboid, clan ST). They are integral membrane proteins related to the Drosophila melanogaster (Fruit fly) rhomboid protein SWISSPROT. Members of this family are found in archaea, bacteria and eukaryotes.

The D. melanogaster rhomboid protease cleaves type-1 transmembrane domains using a catalytic triad composed of serine, histidine and asparagine contributed by different transmembrane domains. It cleaves the transmembrane proteins Spitz, Gurken and Keren within their transmembrane domains to release a soluble TGFalpha-like growth factor. Cleavage occurs in the Golgi, following translocation of the substrates from the endoplasmic reticulum membrane by Star, another transmembrane protein. The growth factors are then able to activate the epidermal growth factor receptor [PUBMED:2110920, PUBMED:11672525].

Few substrates of mammalian rhomboid homologues have been determined, but rhomboid-like protein 2 has been shown to cleave ephrin B3 [PUBMED:15047175]. Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite.

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan Rhomboid-like (CL0207), which has the following description:

This clan contains proteins from both bacteria and eukaryotes. The Rhomboid protein is an intramembrane serine protease which is involved in epidermal growth factor (EGF)-dependent signalling pathways [1]. The DER1 family is involved in degradation of misfolded ER proteins [2].

The clan contains the following 3 members:

DER1 DUF1751 Rhomboid

Alignments

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(62)
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(2099)
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(1081)
RP35
(2524)
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RP75
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(62)
Full
(29346)
Representative proteomes NCBI
(16649)
Meta
(2099)
RP15
(1081)
RP35
(2524)
RP55
(3653)
RP75
(4558)
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  Seed
(62)
Full
(29346)
Representative proteomes NCBI
(16649)
Meta
(2099)
RP15
(1081)
RP35
(2524)
RP55
(3653)
RP75
(4558)
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Trees

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1399 (release 4.1)
Previous IDs: none
Type: Family
Author: Sohrmann M, Bateman A
Number in seed: 62
Number in full: 29346
Average length of the domain: 147.60 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 46.86 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.2 22.2
Trusted cut-off 22.2 22.2
Noise cut-off 22.1 22.1
Model length: 147
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 3 interactions for this family. More...

Rhomboid_N Rhomboid_N Rhomboid

Structures

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 domain has been found. There are 27 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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