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Conserved domains on  [gi|2099853791|gb|UBK05837|]
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interphotoreceptor retinoid-binding protein, partial [Spicara flexuosa]

Protein Classification

S41 family peptidase( domain architecture ID 10165999)

S41 family peptidase similar to vertebrate retinol-binding protein 3 (Rbp3), the major soluble component of the interphotoreceptor matrix and is critical to the function, integrity, and development of the retina

CATH:  3.90.226.10|3.30.750.44
EC:  3.4.-.-
Gene Ontology:  GO:0006508|GO:0008236
MEROPS:  S41

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 1-126 1.68e-43

Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium (RPE). IRBP is secreted by photoreceptors into the interphotoreceptor matrix (IPM) where it is rapidly turned over by a combination of RPE and photoreceptor endocytosis. It is the most abundant soluble protein component of the IPM, consisting of homologous modules, each repeat structure arising through the duplication (as in teleost IRBP) or quadruplication (in tetrapods) of an ancient gene, arisen in the early evolution of the vertebrate eye. IRBP has been shown to promote the release of all-trans retinol from photoreceptors and facilitates its delivery to the RPE. Conversely, IRBP can promote the release of 11-cis-retinal from the RPE, prevent its isomerization in the subretinal space, and transfer it to photoreceptors. In vivo evidence implicates IRBP as a retinoid transporter in the visual cycle, suggesting a critical role for IRBP in cone function essential for human vision. IRBP is a dominant autoimmune antigen in the eye; IRBP proteolysis analysis has proven a useful biomarker for autoimmune uveitis (AU) disorders, a major cause of blindness. This family also includes a chlamydia-secreted protein, designated chlamydia protease-like activity factor (CPAF), known to degrade host proteins, enabling Chlamydia to evade host defenses and replicate.


:

Pssm-ID: 143479 [Multi-domain]  Cd Length: 250  Bit Score: 142.43  E-value: 1.68e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791   1 GYLRIDHILGDEVADkiGPLLLDLVWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPQLHIDSVYDRPSNTTTKL 80
Cdd:cd07563    66 GYLRIDSFGGFEIAA--AEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTEL 143

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2099853791  81 LSMDTLLGERYGVTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:cd07563   144 WTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVG 189
 
Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 1-126 1.68e-43

Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium (RPE). IRBP is secreted by photoreceptors into the interphotoreceptor matrix (IPM) where it is rapidly turned over by a combination of RPE and photoreceptor endocytosis. It is the most abundant soluble protein component of the IPM, consisting of homologous modules, each repeat structure arising through the duplication (as in teleost IRBP) or quadruplication (in tetrapods) of an ancient gene, arisen in the early evolution of the vertebrate eye. IRBP has been shown to promote the release of all-trans retinol from photoreceptors and facilitates its delivery to the RPE. Conversely, IRBP can promote the release of 11-cis-retinal from the RPE, prevent its isomerization in the subretinal space, and transfer it to photoreceptors. In vivo evidence implicates IRBP as a retinoid transporter in the visual cycle, suggesting a critical role for IRBP in cone function essential for human vision. IRBP is a dominant autoimmune antigen in the eye; IRBP proteolysis analysis has proven a useful biomarker for autoimmune uveitis (AU) disorders, a major cause of blindness. This family also includes a chlamydia-secreted protein, designated chlamydia protease-like activity factor (CPAF), known to degrade host proteins, enabling Chlamydia to evade host defenses and replicate.


Pssm-ID: 143479 [Multi-domain]  Cd Length: 250  Bit Score: 142.43  E-value: 1.68e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791   1 GYLRIDHILGDEVADkiGPLLLDLVWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPQLHIDSVYDRPSNTTTKL 80
Cdd:cd07563    66 GYLRIDSFGGFEIAA--AEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTEL 143

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2099853791  81 LSMDTLLGERYGVTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:cd07563   144 WTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVG 189
TSPc smart00245
tail specific protease; tail specific protease
 1-126 2.20e-26

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 96.94  E-value: 2.20e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791    1 GYLRIdHILGDEVADKIGPLLLDL---VWNKILPT--SALIFDLRYTSSGDISGIPYIVSYFTQAEPqlHIDSVYDRpsn 75
Cdd:smart00245  23 GYLRF-GFIGYIRIPEFSEHTSNLvekAWKKLEKTnvEGLILDLRNNPGGLLSAAIDVSSLFLDKGV--IVYTVYRR--- 96

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2099853791   76 tTTKLLSMDTLLGERYgvTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:smart00245  97 -TGELWTYPANLGRKY--SKPLVVLVNKGTASASEIFAGALKDLGRATIVG 144
Peptidase_S41 pfam03572
Peptidase family S41;
1-126 6.79e-07

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 45.67  E-value: 6.79e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791   1 GYLRI---DHILGDEVADKIGPLlldlvwnKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPqlhIDSVYDRPSNTT 77
Cdd:pfam03572   3 GYIRIpsfSEKTAKELAEALKEL-------KKQGVKGLILDLRGNPGGLLSAAVEIASLFLPDGT---IVSTRGRDGSKE 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2099853791  78 TKLlsmDTLLGERYGVTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:pfam03572  73 VYF---AAGKADEVLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVG 118
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 1-126 8.41e-07

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440556 [Multi-domain]  Cd Length: 341  Bit Score: 46.02  E-value: 8.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791   1 GYLRIDHiLGDEVADKIGPLLLDLVWNKIlptSALIFDLRYTSSGDISGIPYIVSYFTQAEPQlhidsVYDRPSNTTTKL 80
Cdd:COG0793   160 GYIRIPS-FGENTAEEFKRALKELKKQGA---KGLILDLRNNPGGLLDEAVELADLFLPKGPI-----VYTRGRNGKVET 230

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2099853791  81 LSMDtllGERYGVTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:COG0793   231 YKAT---PGGALYDGPLVVLVNEGSASASEIFAGALQDYGRGVIVG 273
 
Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 1-126 1.68e-43

Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium (RPE). IRBP is secreted by photoreceptors into the interphotoreceptor matrix (IPM) where it is rapidly turned over by a combination of RPE and photoreceptor endocytosis. It is the most abundant soluble protein component of the IPM, consisting of homologous modules, each repeat structure arising through the duplication (as in teleost IRBP) or quadruplication (in tetrapods) of an ancient gene, arisen in the early evolution of the vertebrate eye. IRBP has been shown to promote the release of all-trans retinol from photoreceptors and facilitates its delivery to the RPE. Conversely, IRBP can promote the release of 11-cis-retinal from the RPE, prevent its isomerization in the subretinal space, and transfer it to photoreceptors. In vivo evidence implicates IRBP as a retinoid transporter in the visual cycle, suggesting a critical role for IRBP in cone function essential for human vision. IRBP is a dominant autoimmune antigen in the eye; IRBP proteolysis analysis has proven a useful biomarker for autoimmune uveitis (AU) disorders, a major cause of blindness. This family also includes a chlamydia-secreted protein, designated chlamydia protease-like activity factor (CPAF), known to degrade host proteins, enabling Chlamydia to evade host defenses and replicate.


Pssm-ID: 143479 [Multi-domain]  Cd Length: 250  Bit Score: 142.43  E-value: 1.68e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791   1 GYLRIDHILGDEVADkiGPLLLDLVWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPQLHIDSVYDRPSNTTTKL 80
Cdd:cd07563    66 GYLRIDSFGGFEIAA--AEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTEL 143

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2099853791  81 LSMDTLLGERYGVTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:cd07563   144 WTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVG 189
TSPc smart00245
tail specific protease; tail specific protease
 1-126 2.20e-26

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 96.94  E-value: 2.20e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791    1 GYLRIdHILGDEVADKIGPLLLDL---VWNKILPT--SALIFDLRYTSSGDISGIPYIVSYFTQAEPqlHIDSVYDRpsn 75
Cdd:smart00245  23 GYLRF-GFIGYIRIPEFSEHTSNLvekAWKKLEKTnvEGLILDLRNNPGGLLSAAIDVSSLFLDKGV--IVYTVYRR--- 96

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2099853791   76 tTTKLLSMDTLLGERYgvTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:smart00245  97 -TGELWTYPANLGRKY--SKPLVVLVNKGTASASEIFAGALKDLGRATIVG 144
Peptidase_S41 cd06567
C-terminal processing peptidase family S41; Peptidase family S41 (C-terminal processing ...
 1-126 9.04e-19

C-terminal processing peptidase family S41; Peptidase family S41 (C-terminal processing peptidase or CTPase family) contains very different subfamilies; it includes photosystem II D1 C-terminal processing protease (CTPase), interphotoreceptor retinoid-binding protein IRBP and tricorn protease (TRI). CTPase and TRI both contain the PDZ domain while IRBP, although being very similar to the tail-specific protease domain, lacks the PDZ insertion domain and hydrolytic activity. These serine proteases have distinctly different active sites: in CTPase, the active site consists of a serine/lysine catalytic dyad while in tricorn core protease, it is a tetrad (serine, histidine, serine, glutamate). CPases with different substrate specificities in different species include processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein; and others such as tricorn protease (TRI) act as a carboxypeptidase, involved in the degradation of proteasomal products. CTPase homolog IRBP, secreted by photoreceptors into the interphotoreceptor matrix, having arisen in the early evolution of the vertebrate eye, promotes the release of all-trans retinol from photoreceptors and facilitates its delivery to the retinal pigment epithelium.


Pssm-ID: 143475 [Multi-domain]  Cd Length: 224  Bit Score: 78.11  E-value: 9.04e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791   1 GYLRIDHILGDEVADkigpLLLDLVWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPQLHIDSVYDRPSNTTTKL 80
Cdd:cd06567    62 GYIRIPSFSAESTAE----ELREALAELKKGVKGLILDLRNNPGGLLSAAVELASLFLPKGKIVVTTRRRGGNETEYVAP 137

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2099853791  81 lsmdtllGERYGVTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:cd06567   138 -------GGGSLYDGPLVVLVNEGSASASEIFAGALQDLGRATLVG 176
Peptidase_S41 pfam03572
Peptidase family S41;
1-126 6.79e-07

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 45.67  E-value: 6.79e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791   1 GYLRI---DHILGDEVADKIGPLlldlvwnKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPqlhIDSVYDRPSNTT 77
Cdd:pfam03572   3 GYIRIpsfSEKTAKELAEALKEL-------KKQGVKGLILDLRGNPGGLLSAAVEIASLFLPDGT---IVSTRGRDGSKE 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2099853791  78 TKLlsmDTLLGERYGVTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:pfam03572  73 VYF---AAGKADEVLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVG 118
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 1-126 8.41e-07

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440556 [Multi-domain]  Cd Length: 341  Bit Score: 46.02  E-value: 8.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791   1 GYLRIDHiLGDEVADKIGPLLLDLVWNKIlptSALIFDLRYTSSGDISGIPYIVSYFTQAEPQlhidsVYDRPSNTTTKL 80
Cdd:COG0793   160 GYIRIPS-FGENTAEEFKRALKELKKQGA---KGLILDLRNNPGGLLDEAVELADLFLPKGPI-----VYTRGRNGKVET 230

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2099853791  81 LSMDtllGERYGVTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:COG0793   231 YKAT---PGGALYDGPLVVLVNEGSASASEIFAGALQDYGRGVIVG 273
Peptidase_S41_TRI cd07562
Tricorn protease; serine protease family S41; The tricorn protease (TRI), a member of the S41 ...
 1-126 1.01e-05

Tricorn protease; serine protease family S41; The tricorn protease (TRI), a member of the S41 peptidase family and named for its tricorn-like shape, exists only in some archaea and eubacteria. It has been shown to act as a carboxypeptidase, involved in the degradation of proteasomal products to preferentially yield di- and tripeptides, with subsequent and final degradations to free amino acid residues by tricorn interacting factors, F1, F2 and F3. Tricorn is a hexameric D3-symmetric protease of 720kD, and can self-associate further into a giant icosahedral capsid structure containing twenty copies of the complex. Each tricorn peptidase monomer consists of five structural domains: a six-bladed beta-propeller and a seven-bladed beta-propeller that limit access to the active site, the two domains (C1 and C2) that carry the active site residues, and a PDZ-like domain (proposed to be important for substrate recognition) between the C1 and C2 domains. The active site tetrad residues are distributed between the C1 and C2 domains, with serine and histidine on C1 and serine and glutamate on C2.


Pssm-ID: 143478 [Multi-domain]  Cd Length: 266  Bit Score: 42.96  E-value: 1.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099853791   1 GYLRIDHILGDEvadkigpllLDLVWNKILPTS---ALIFDLRYTSSGDISGipYIVSYFTQAEPQLHIDSVYDRPSNTT 77
Cdd:cd07562    90 GYVHIPDMGDDG---------FAEFLRDLLAEVdkdGLIIDVRFNGGGNVAD--LLLDFLSRRRYGYDIPRGGGKPVTYP 158

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2099853791  78 tkllsmdtllgeRYGVTKPLIILTSKNTKGIAEDVAYCLQNLKRATIVG 126
Cdd:cd07562   159 ------------SGRWRGPVVVLVNEGSASDAEIFAYGFRALGLGPVVG 195
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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