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Conserved domains on  [gi|4235328|gb|AAD13172|]
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interphotoreceptor retinoid binding protein precursor, partial [Varecia rubra]

Protein Classification

interphotoreceptor retinoid-binding protein( domain architecture ID 10166016)

interphotoreceptor retinoid-binding protein (IRBP) is a large glycoprotein known to bind retinoids and found primarily in the interphotoreceptor matrix of the retina between the retinal pigment epithelium and the photoreceptor cells

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 ...
 27-214 5.38e-66

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: 207.53  E-value: 5.38e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328   27 VGYLRVDDIPGEEVlsKLGQFLVAHVWGKLMGTSALVLDLRHCTGGQVSGIPYVISYLHPGNTVLHVDTIYDRPSNTTKE 106
Cdd:cd07563  65 IGYLRIDSFGGFEI--AAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTE 142

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328  107 IWTLPQVPGERYGADKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLRIGQsNFFLTVPVSRSLGPL 186
Cdd:cd07563 143 LWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSVDPI 221

                       170       180
                ....*....|....*....|....*...
gi 4235328  187 GGGSqtWEGSGVLPCVGTPAEQALEKAL 214
Cdd:cd07563 222 TGTN--WEGVGVPPDIEVPATPGYDDAL 247
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 206-312 3.69e-48

N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterized as a serine-peptidase, pfam03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B.


:

Pssm-ID: 463396  Cd Length: 129  Bit Score: 157.48  E-value: 3.69e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328    206 AEQALEKALSILTLRRALPGVVRCLQEALQDHYTLVDRVPTLQNHLASM----DFSTVVSEEDLVTKLNAGLQAVSEDPR 281
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLlasgDYSSVVSEEDLASKLNADLQALSGDPR 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 4235328    282 LLVRAIGPRETPPGPEAEaEELPGEVPEVPE 312
Cdd:pfam11918  81 LKVRYIRPEPASDEPEAA-DNIPGLVPMQPP 110
 
Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 27-214 5.38e-66

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: 207.53  E-value: 5.38e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328   27 VGYLRVDDIPGEEVlsKLGQFLVAHVWGKLMGTSALVLDLRHCTGGQVSGIPYVISYLHPGNTVLHVDTIYDRPSNTTKE 106
Cdd:cd07563  65 IGYLRIDSFGGFEI--AAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTE 142

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328  107 IWTLPQVPGERYGADKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLRIGQsNFFLTVPVSRSLGPL 186
Cdd:cd07563 143 LWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSVDPI 221

                       170       180
                ....*....|....*....|....*...
gi 4235328  187 GGGSqtWEGSGVLPCVGTPAEQALEKAL 214
Cdd:cd07563 222 TGTN--WEGVGVPPDIEVPATPGYDDAL 247
TSPc smart00245
tail specific protease; tail specific protease
 6-205 1.57e-53

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 173.60  E-value: 1.57e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328       6 TQEELLTWLQRGLRYEVLEGNVGYLRVDDIpGEEVLSKLGQ---FLVAHVWGKLMGT--SALVLDLRHCTGGQVSGIPYV 80
Cdd:smart00245   1 SKERTIALIRDKIKIETLEGNVGYLRFGFI-GYIRIPEFSEhtsNLVEKAWKKLEKTnvEGLILDLRNNPGGLLSAAIDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328      81 ISYLHPGNTvlHVDTIYDRpsntTKEIWTLPQVPGERYgaDKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGA 160
Cdd:smart00245  80 SSLFLDKGV--IVYTVYRR----TGELWTYPANLGRKY--SKPLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKG 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 4235328     161 LNLQKLRIGqSNFFLTVPVSRSLGPLGggsQTWEGSGVLPCVGTP 205
Cdd:smart00245 152 LVQQTVPLG-DGSGLKLTVAKYYTPSG---KSIEKKGVEPDIQVP 192
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 206-312 3.69e-48

N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterized as a serine-peptidase, pfam03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B.


Pssm-ID: 463396  Cd Length: 129  Bit Score: 157.48  E-value: 3.69e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328    206 AEQALEKALSILTLRRALPGVVRCLQEALQDHYTLVDRVPTLQNHLASM----DFSTVVSEEDLVTKLNAGLQAVSEDPR 281
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLlasgDYSSVVSEEDLASKLNADLQALSGDPR 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 4235328    282 LLVRAIGPRETPPGPEAEaEELPGEVPEVPE 312
Cdd:pfam11918  81 LKVRYIRPEPASDEPEAA-DNIPGLVPMQPP 110
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 19-200 1.72e-16

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: 78.76  E-value: 1.72e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328   19 RYEVLEGNVGYLRVDDI---PGEEVLSKLGQFlvahvwgKLMGTSALVLDLRHCTGGQVSGIPYVISYLHPGNTVLhvdt 95
Cdd:COG0793 151 EAKLLEGKIGYIRIPSFgenTAEEFKRALKEL-------KKQGAKGLILDLRNNPGGLLDEAVELADLFLPKGPIV---- 219

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328   96 iYDRPSNttKEIWTLPQVPGERYgADKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGAlnlqklrIGQSNF-- 173
Cdd:COG0793 220 -YTRGRN--GKVETYKATPGGAL-YDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGKG-------SVQTVFpl 288

                       170       180       190
                ....*....|....*....|....*....|.
gi 4235328  174 ----FLTVPVSRSLGPLGGGsqtWEGSGVLP 200
Cdd:COG0793 289 pdggALKLTTARYYTPSGRS---IQGKGVEP 316
Peptidase_S41 pfam03572
Peptidase family S41;
26-200 4.83e-12

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 63.01  E-value: 4.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328     26 NVGYLRVDDI---PGEEVLSKLGQFlvahvwgKLMGTSALVLDLRHCTGGQVSGIPYVISYLHPGNTVLHVDtiyDRPSN 102
Cdd:pfam03572   1 KIGYIRIPSFsekTAKELAEALKEL-------KKQGVKGLILDLRGNPGGLLSAAVEIASLFLPDGTIVSTR---GRDGS 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328    103 TTKEIWTLPQVPgerYGADKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGALnLQKLRIGQSNFFLTVPVSRS 182
Cdd:pfam03572  71 KEVYFAAGKADE---VLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVGERTFGKGT-VQTVYPLPDGSALKLTIAKY 146

                         170
                  ....*....|....*...
gi 4235328    183 LGPlGGGSQtwEGSGVLP 200
Cdd:pfam03572 147 YTP-DGRSI--EGKGIEP 161
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 226-288 5.68e-06

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: 46.90  E-value: 5.68e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4235328  226 VVRCLQEALQDHY----TLVDRVPTLQNHLASMDFSTVVSEEDLVTKLNAGLQAVsEDPRLLVRAIG 288
Cdd:cd07563   1 VFEALAKLLEENYafpeAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQEL-GDGHLNVSYIG 66
 
Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 27-214 5.38e-66

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: 207.53  E-value: 5.38e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328   27 VGYLRVDDIPGEEVlsKLGQFLVAHVWGKLMGTSALVLDLRHCTGGQVSGIPYVISYLHPGNTVLHVDTIYDRPSNTTKE 106
Cdd:cd07563  65 IGYLRIDSFGGFEI--AAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTE 142

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328  107 IWTLPQVPGERYGADKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLRIGQsNFFLTVPVSRSLGPL 186
Cdd:cd07563 143 LWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSVDPI 221

                       170       180
                ....*....|....*....|....*...
gi 4235328  187 GGGSqtWEGSGVLPCVGTPAEQALEKAL 214
Cdd:cd07563 222 TGTN--WEGVGVPPDIEVPATPGYDDAL 247
TSPc smart00245
tail specific protease; tail specific protease
 6-205 1.57e-53

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 173.60  E-value: 1.57e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328       6 TQEELLTWLQRGLRYEVLEGNVGYLRVDDIpGEEVLSKLGQ---FLVAHVWGKLMGT--SALVLDLRHCTGGQVSGIPYV 80
Cdd:smart00245   1 SKERTIALIRDKIKIETLEGNVGYLRFGFI-GYIRIPEFSEhtsNLVEKAWKKLEKTnvEGLILDLRNNPGGLLSAAIDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328      81 ISYLHPGNTvlHVDTIYDRpsntTKEIWTLPQVPGERYgaDKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGA 160
Cdd:smart00245  80 SSLFLDKGV--IVYTVYRR----TGELWTYPANLGRKY--SKPLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKG 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 4235328     161 LNLQKLRIGqSNFFLTVPVSRSLGPLGggsQTWEGSGVLPCVGTP 205
Cdd:smart00245 152 LVQQTVPLG-DGSGLKLTVAKYYTPSG---KSIEKKGVEPDIQVP 192
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 206-312 3.69e-48

N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterized as a serine-peptidase, pfam03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B.


Pssm-ID: 463396  Cd Length: 129  Bit Score: 157.48  E-value: 3.69e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328    206 AEQALEKALSILTLRRALPGVVRCLQEALQDHYTLVDRVPTLQNHLASM----DFSTVVSEEDLVTKLNAGLQAVSEDPR 281
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLlasgDYSSVVSEEDLASKLNADLQALSGDPR 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 4235328    282 LLVRAIGPRETPPGPEAEaEELPGEVPEVPE 312
Cdd:pfam11918  81 LKVRYIRPEPASDEPEAA-DNIPGLVPMQPP 110
Peptidase_S41 cd06567
C-terminal processing peptidase family S41; Peptidase family S41 (C-terminal processing ...
 26-202 1.59e-31

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: 117.40  E-value: 1.59e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328   26 NVGYLRVDDIPGEEVLSKLGQFLVAhvwgKLMGTSALVLDLRHCTGGQVSGIPYVISYLHPGNTVLHVDTIYDRPsnttk 105
Cdd:cd06567  60 TIGYIRIPSFSAESTAEELREALAE----LKKGVKGLILDLRNNPGGLLSAAVELASLFLPKGKIVVTTRRRGGN----- 130

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328  106 eiWTLPQVPGERYGADKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGALNlQKLRIGQSNFFLTVPVSRSLGP 185
Cdd:cd06567 131 --ETEYVAPGGGSLYDGPLVVLVNEGSASASEIFAGALQDLGRATLVGERTFGKGSV-QTVFPLLDGSALKLTTAKYYTP 207

                       170
                ....*....|....*..
gi 4235328  186 LGGgsqTWEGSGVLPCV 202
Cdd:cd06567 208 SGR---SIEGKGVEPDI 221
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 19-200 1.72e-16

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: 78.76  E-value: 1.72e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328   19 RYEVLEGNVGYLRVDDI---PGEEVLSKLGQFlvahvwgKLMGTSALVLDLRHCTGGQVSGIPYVISYLHPGNTVLhvdt 95
Cdd:COG0793 151 EAKLLEGKIGYIRIPSFgenTAEEFKRALKEL-------KKQGAKGLILDLRNNPGGLLDEAVELADLFLPKGPIV---- 219

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328   96 iYDRPSNttKEIWTLPQVPGERYgADKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGAlnlqklrIGQSNF-- 173
Cdd:COG0793 220 -YTRGRN--GKVETYKATPGGAL-YDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGKG-------SVQTVFpl 288

                       170       180       190
                ....*....|....*....|....*....|.
gi 4235328  174 ----FLTVPVSRSLGPLGGGsqtWEGSGVLP 200
Cdd:COG0793 289 pdggALKLTTARYYTPSGRS---IQGKGVEP 316
Peptidase_S41_TRI cd07562
Tricorn protease; serine protease family S41; The tricorn protease (TRI), a member of the S41 ...
 24-200 2.80e-13

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: 68.38  E-value: 2.80e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328   24 EGNVGYLRVDDIPGEEVlsklgqflvAHVWGKLMGTS---ALVLDLRHCTGGQVSGipYVISYLHPGNTvlhvdtIYDRP 100
Cdd:cd07562  86 DGRIGYVHIPDMGDDGF---------AEFLRDLLAEVdkdGLIIDVRFNGGGNVAD--LLLDFLSRRRY------GYDIP 148

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328  101 SNTTKEIWTlpqvPGERYgaDKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLR-IGQSnfFLTVPV 179
Cdd:cd07562 149 RGGGKPVTY----PSGRW--RGPVVVLVNEGSASDAEIFAYGFRALGLGPVVGTRTAGGVIISGRYRlPDGG--SLTVPE 220

                       170       180
                ....*....|....*....|.
gi 4235328  180 SRSLGPLGGGSqtwEGSGVLP 200
Cdd:cd07562 221 FGVYLPDGGPL---ENRGVAP 238
Peptidase_S41 pfam03572
Peptidase family S41;
26-200 4.83e-12

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 63.01  E-value: 4.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328     26 NVGYLRVDDI---PGEEVLSKLGQFlvahvwgKLMGTSALVLDLRHCTGGQVSGIPYVISYLHPGNTVLHVDtiyDRPSN 102
Cdd:pfam03572   1 KIGYIRIPSFsekTAKELAEALKEL-------KKQGVKGLILDLRGNPGGLLSAAVEIASLFLPDGTIVSTR---GRDGS 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235328    103 TTKEIWTLPQVPgerYGADKDVVVLTSGRTGGVAEDIAYILKQMRRAIVVGERTVGGALnLQKLRIGQSNFFLTVPVSRS 182
Cdd:pfam03572  71 KEVYFAAGKADE---VLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVGERTFGKGT-VQTVYPLPDGSALKLTIAKY 146

                         170
                  ....*....|....*...
gi 4235328    183 LGPlGGGSQtwEGSGVLP 200
Cdd:pfam03572 147 YTP-DGRSI--EGKGIEP 161
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 226-288 5.68e-06

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: 46.90  E-value: 5.68e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4235328  226 VVRCLQEALQDHY----TLVDRVPTLQNHLASMDFSTVVSEEDLVTKLNAGLQAVsEDPRLLVRAIG 288
Cdd:cd07563   1 VFEALAKLLEENYafpeAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQEL-GDGHLNVSYIG 66
 
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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