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Conserved domains on  [gi|256220954|ref|NP_001035161|]
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protein NYNRIN [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_N4BP1-like cd18728
PRORP-like PIN domain of NEDD4 binding protein 1 and related proteins; NEDD4-binding partner-1 ...
 743-867 9.50e-74

PRORP-like PIN domain of NEDD4 binding protein 1 and related proteins; NEDD4-binding partner-1 (N4BP1) interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. This subfamily additionally includes NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. This subfamily belongs to the Zc3h12a-N4BP1-like PIN subfamily of the PRORP-Zc3h12a-like PIN family, the latter of which additionally includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


:

Pssm-ID: 350295  Cd Length: 127  Bit Score: 241.25  E-value: 9.50e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954  743 VVIDGSSVAMVHGLQHFFSCRGIAMAVQYFWNRGHREITVFVPTWQLKKNRRVRESHFLTKLHRLKMLSITPSQLENGKK 822
Cdd:cd18728     1 IVIDGSNVAMVHGLQHFFSCRGIAIAVEYFWKRGHRNITVFVPQWRTKRDPNVTEQHFLTQLQELGILSLTPSRMVLGKR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 256220954  823 ITTYDYRFMVKLAEETDGVIVTNEQIHILMNNS--KKLMVKDRLLPF 867
Cdd:cd18728    81 IASHDDRFLLHLAEKTGGIIVTNDNFREFVNESpsWREIIKERLLQY 127
KH-I_NYNRIN_like cd22477
type I K homology (KH) RNA-binding domain found in the subfamily of NYN domain and retroviral ...
 75-140 1.51e-35

type I K homology (KH) RNA-binding domain found in the subfamily of NYN domain and retroviral integrase catalytic domain-containing protein (NYNRIN); The NYNRIN subfamily includes NYNRIN and KH and NYN domain-containing protein (KHNYN). NYNRIN, also known as CGIN1/Cousin of GIN1, may contribute to retroviral resistance in mammals by regulating the ubiquitination of viral proteins. KHNYN acts as a novel cofactor for zinc finger antiviral protein (ZAP) to target CpG-containing retroviral RNA for degradation.


:

Pssm-ID: 411905  Cd Length: 66  Bit Score: 129.83  E-value: 1.51e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 256220954   75 PELWKEVRYPPVLHCAFLGAQGLFLDCLCWSTLAYLVPGPPGSLMVGGLTESFTMTQNWLEELVAR 140
Cdd:cd22477     1 PELTKEVLYPRDLHCIFLGAKGLFLDCLIWGTSAHIVPGAPGSLLISGLTEAFVMAQSRIEDLVEK 66
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1073-1173 6.52e-20

RNase H-like domain found in reverse transcriptase;


:

Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 86.40  E-value: 6.52e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954  1073 WNQEHEKSFLALKRALVCALCLSTPNPNLPFYLEVTVSQVSLTASLHQEHS-GRKHPIAYTSKPLLPDE------DSEGp 1145
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdGGERPIAYASRKLSPAErnysttEKEL- 79

                           90       100
                   ....*....|....*....|....*...
gi 256220954  1146 qsggdspYAVAWALKHFARCVGDNPVVL 1173
Cdd:pfam17919   80 -------LAIVFALKKFRHYLLGRKFTV 100
KH-I_N4BP1_like_rpt1 cd09032
first type I K homology (KH) RNA-binding domain found in the family of NEDD4-binding protein 1 ...
 12-73 7.59e-19

first type I K homology (KH) RNA-binding domain found in the family of NEDD4-binding protein 1 (N4BP1); The N4BP1 family includes N4BP1, NYN domain and retroviral integrase catalytic domain-containing protein (NYNRIN) and KH and NYN domain-containing protein (KHNYN). These proteins are probably of retroviral origin. N4BP1 interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally downregulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. N4BP1 acts by interacting with the second WW domain of ITCH, leading to compete with ITCH's substrates and impairing ubiquitination of substrates. NYNRIN, also known as CGIN1/Cousin of GIN1, may contribute to retroviral resistance in mammals by regulating the ubiquitination of viral proteins. KHNYN acts as a novel cofactor for zinc finger antiviral protein (ZAP) to target CpG-containing retroviral RNA for degradation. Members of this family contains two type I K homology (KH) RNA-binding domain. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411808  Cd Length: 65  Bit Score: 81.95  E-value: 7.59e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 256220954   12 EWFMVQTKSKPRVHRQRLQVQRIFRVKVT---AFQSRPDTPYFWLQLEGPRENTGKAKEYLKGLC 73
Cdd:cd09032     1 DEFVVPAEKVPLLERSRPRIERLFGVKVSlleELSKPKDGGKQWVQLEGDEEDVRKAKEYIKALC 65
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1479-1532 1.96e-14

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 69.20  E-value: 1.96e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 256220954  1479 VPRQLRRDLIFSVHDSpiGEHQGLEDTYKTVRLLGWWPGMQDHVRDYCRSCLFC 1532
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETC 52
 
Name Accession Description Interval E-value
PIN_N4BP1-like cd18728
PRORP-like PIN domain of NEDD4 binding protein 1 and related proteins; NEDD4-binding partner-1 ...
 743-867 9.50e-74

PRORP-like PIN domain of NEDD4 binding protein 1 and related proteins; NEDD4-binding partner-1 (N4BP1) interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. This subfamily additionally includes NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. This subfamily belongs to the Zc3h12a-N4BP1-like PIN subfamily of the PRORP-Zc3h12a-like PIN family, the latter of which additionally includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350295  Cd Length: 127  Bit Score: 241.25  E-value: 9.50e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954  743 VVIDGSSVAMVHGLQHFFSCRGIAMAVQYFWNRGHREITVFVPTWQLKKNRRVRESHFLTKLHRLKMLSITPSQLENGKK 822
Cdd:cd18728     1 IVIDGSNVAMVHGLQHFFSCRGIAIAVEYFWKRGHRNITVFVPQWRTKRDPNVTEQHFLTQLQELGILSLTPSRMVLGKR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 256220954  823 ITTYDYRFMVKLAEETDGVIVTNEQIHILMNNS--KKLMVKDRLLPF 867
Cdd:cd18728    81 IASHDDRFLLHLAEKTGGIIVTNDNFREFVNESpsWREIIKERLLQY 127
RNase_Zc3h12a pfam11977
Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has ...
 739-890 3.41e-71

Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes. It has been suggested that this domain belongs to the PIN domain superfamily. This domain has also been identified as part of the NYN domain family.


Pssm-ID: 403256  Cd Length: 154  Bit Score: 234.91  E-value: 3.41e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954   739 GLRRVVIDGSSVAMVHGLQHFFSCRGIAMAVQYFWNRGHREITVFVPTWQLKKNRRVRESHFLTKLHRLKMLSITPSQLE 818
Cdd:pfam11977    1 GLRPIVIDGSNVAMSHGRQKKFSVRGLAIAVDYFVKRGHEEITVFVPQWRKEADEKITDQHELLELERLGLIVFTPSRTL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 256220954   819 NGKKITTYDYRFMVKLAEETDGVIVTNEQIHILMNNSKKLM--VKDRLLPFTFAGSLFMVPDDPLGRDGPTLEE 890
Cdd:pfam11977   81 DGKRIVSYDDRFILKLAEETDGVIVSNDNFRDLADENPEWIdiVEERLLMYTFVGDKFMPPDDPLGRVGPSLED 154
KH-I_NYNRIN_like cd22477
type I K homology (KH) RNA-binding domain found in the subfamily of NYN domain and retroviral ...
 75-140 1.51e-35

type I K homology (KH) RNA-binding domain found in the subfamily of NYN domain and retroviral integrase catalytic domain-containing protein (NYNRIN); The NYNRIN subfamily includes NYNRIN and KH and NYN domain-containing protein (KHNYN). NYNRIN, also known as CGIN1/Cousin of GIN1, may contribute to retroviral resistance in mammals by regulating the ubiquitination of viral proteins. KHNYN acts as a novel cofactor for zinc finger antiviral protein (ZAP) to target CpG-containing retroviral RNA for degradation.


Pssm-ID: 411905  Cd Length: 66  Bit Score: 129.83  E-value: 1.51e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 256220954   75 PELWKEVRYPPVLHCAFLGAQGLFLDCLCWSTLAYLVPGPPGSLMVGGLTESFTMTQNWLEELVAR 140
Cdd:cd22477     1 PELTKEVLYPRDLHCIFLGAKGLFLDCLIWGTSAHIVPGAPGSLLISGLTEAFVMAQSRIEDLVEK 66
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1073-1173 6.52e-20

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 86.40  E-value: 6.52e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954  1073 WNQEHEKSFLALKRALVCALCLSTPNPNLPFYLEVTVSQVSLTASLHQEHS-GRKHPIAYTSKPLLPDE------DSEGp 1145
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdGGERPIAYASRKLSPAErnysttEKEL- 79

                           90       100
                   ....*....|....*....|....*...
gi 256220954  1146 qsggdspYAVAWALKHFARCVGDNPVVL 1173
Cdd:pfam17919   80 -------LAIVFALKKFRHYLLGRKFTV 100
KH-I_N4BP1_like_rpt1 cd09032
first type I K homology (KH) RNA-binding domain found in the family of NEDD4-binding protein 1 ...
 12-73 7.59e-19

first type I K homology (KH) RNA-binding domain found in the family of NEDD4-binding protein 1 (N4BP1); The N4BP1 family includes N4BP1, NYN domain and retroviral integrase catalytic domain-containing protein (NYNRIN) and KH and NYN domain-containing protein (KHNYN). These proteins are probably of retroviral origin. N4BP1 interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally downregulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. N4BP1 acts by interacting with the second WW domain of ITCH, leading to compete with ITCH's substrates and impairing ubiquitination of substrates. NYNRIN, also known as CGIN1/Cousin of GIN1, may contribute to retroviral resistance in mammals by regulating the ubiquitination of viral proteins. KHNYN acts as a novel cofactor for zinc finger antiviral protein (ZAP) to target CpG-containing retroviral RNA for degradation. Members of this family contains two type I K homology (KH) RNA-binding domain. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411808  Cd Length: 65  Bit Score: 81.95  E-value: 7.59e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 256220954   12 EWFMVQTKSKPRVHRQRLQVQRIFRVKVT---AFQSRPDTPYFWLQLEGPRENTGKAKEYLKGLC 73
Cdd:cd09032     1 DEFVVPAEKVPLLERSRPRIERLFGVKVSlleELSKPKDGGKQWVQLEGDEEDVRKAKEYIKALC 65
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1479-1532 1.96e-14

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 69.20  E-value: 1.96e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 256220954  1479 VPRQLRRDLIFSVHDSpiGEHQGLEDTYKTVRLLGWWPGMQDHVRDYCRSCLFC 1532
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETC 52
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1104-1207 6.89e-05

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 44.02  E-value: 6.89e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954 1104 YLEVTVSQVSLTASLHQEHS-GRKHPIAYTSKPLLPDE------DSEGpqsggdspYAVAWALKHFARCVGDNPVVLRls 1176
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAErnysttEKEL--------LAIVWALKKFRHYLLGRPFTVY-- 70

                          90       100       110
                  ....*....|....*....|....*....|....
gi 256220954 1177 yasrttVDNEA---WDSRRASKAWLIRWSLLLQD 1207
Cdd:cd09274    71 ------TDHKAlkyLLTQKDLNGRLARWLLLLSE 98
 
Name Accession Description Interval E-value
PIN_N4BP1-like cd18728
PRORP-like PIN domain of NEDD4 binding protein 1 and related proteins; NEDD4-binding partner-1 ...
 743-867 9.50e-74

PRORP-like PIN domain of NEDD4 binding protein 1 and related proteins; NEDD4-binding partner-1 (N4BP1) interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. This subfamily additionally includes NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. This subfamily belongs to the Zc3h12a-N4BP1-like PIN subfamily of the PRORP-Zc3h12a-like PIN family, the latter of which additionally includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350295  Cd Length: 127  Bit Score: 241.25  E-value: 9.50e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954  743 VVIDGSSVAMVHGLQHFFSCRGIAMAVQYFWNRGHREITVFVPTWQLKKNRRVRESHFLTKLHRLKMLSITPSQLENGKK 822
Cdd:cd18728     1 IVIDGSNVAMVHGLQHFFSCRGIAIAVEYFWKRGHRNITVFVPQWRTKRDPNVTEQHFLTQLQELGILSLTPSRMVLGKR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 256220954  823 ITTYDYRFMVKLAEETDGVIVTNEQIHILMNNS--KKLMVKDRLLPF 867
Cdd:cd18728    81 IASHDDRFLLHLAEKTGGIIVTNDNFREFVNESpsWREIIKERLLQY 127
RNase_Zc3h12a pfam11977
Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has ...
 739-890 3.41e-71

Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes. It has been suggested that this domain belongs to the PIN domain superfamily. This domain has also been identified as part of the NYN domain family.


Pssm-ID: 403256  Cd Length: 154  Bit Score: 234.91  E-value: 3.41e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954   739 GLRRVVIDGSSVAMVHGLQHFFSCRGIAMAVQYFWNRGHREITVFVPTWQLKKNRRVRESHFLTKLHRLKMLSITPSQLE 818
Cdd:pfam11977    1 GLRPIVIDGSNVAMSHGRQKKFSVRGLAIAVDYFVKRGHEEITVFVPQWRKEADEKITDQHELLELERLGLIVFTPSRTL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 256220954   819 NGKKITTYDYRFMVKLAEETDGVIVTNEQIHILMNNSKKLM--VKDRLLPFTFAGSLFMVPDDPLGRDGPTLEE 890
Cdd:pfam11977   81 DGKRIVSYDDRFILKLAEETDGVIVSNDNFRDLADENPEWIdiVEERLLMYTFVGDKFMPPDDPLGRVGPSLED 154
PIN_Zc3h12a-N4BP1-like cd18719
PRORP-like PIN domain of ribonuclease Zc3h12a, NEDD4-binding partner-1, and related proteins; ...
 743-867 3.32e-56

PRORP-like PIN domain of ribonuclease Zc3h12a, NEDD4-binding partner-1, and related proteins; Zc3h12a (zinc finger CCCH-type containing 12A, also known as MCPIP1/MCP induced protein 1 and Regnase-1) is a critical regulator of inflammatory response, with additional roles in defense against viruses and various stresses, cellular differentiation, and apoptosis. This subfamily also includes Caenorhabditis elegans REGE-1 (REGnasE-1), which also functions as a cytoplasmic endonuclease. Additionally, it includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4, as well as N4BP1 (NEDD4-binding partner-1), NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. This subfamily belongs to the PRORP-Zc3h12a-like PIN family which in addition includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350286  Cd Length: 127  Bit Score: 190.88  E-value: 3.32e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954  743 VVIDGSSVAMVHGLQHFFSCRGIAMAVQYFWNRGHrEITVFVPTWQLKKNR-RVRESHFLTKLHRLKMLSITPSQLENGK 821
Cdd:cd18719     1 VVIDGSNVAMSHGNGKVFSCKGIQICVRYFLERGH-EVTAFVPQFRLESPNpNSTDQDILEELERLGILVFTPSRRVPGK 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 256220954  822 KITTYDYRFMVKLAEETDGVIVTNEQIHILMNNSK--KLMVKDRLLPF 867
Cdd:cd18719    80 RISSYDDRFILQLAEETDGVIVSNDNFRDLLNENPdwREIIEERLLPF 127
PIN_Zc3h12-like cd18729
PRORP-like PIN domain of ribonuclease Zc3h12a and related proteins; Zc3h12a (zinc finger ...
 743-868 5.85e-43

PRORP-like PIN domain of ribonuclease Zc3h12a and related proteins; Zc3h12a (zinc finger CCCH-type containing 12A, also known as MCPIP1/MCP induced protein 1 and Regnase-1) is a critical regulator of inflammatory response, with additional roles in defense against viruses and various stresses, cellular differentiation, and apoptosis. This subfamily also includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4. It belongs to the Zc3h12a-N4BP1-like PIN subfamily of the PRORP-Zc3h12a-like PIN family, the latter of which additionally includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350296  Cd Length: 131  Bit Score: 153.29  E-value: 5.85e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954  743 VVIDGSSVAMVHGLQHFFSCRGIAMAVQYFWNRGHREITVFVPTWQlKKNRR----VRESHFLTKLHRLKMLSITPSQLE 818
Cdd:cd18729     1 IVIDGSNVAMSHGNKEVFSCRGIQLAVDWFRERGHRDITVFVPSWR-KEQPRpdapITDQEILRELEKEKILVFTPSRRV 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 256220954  819 NGKKITTYDYRFMVKLAEETDGVIVTNEQIHILMNNSK--KLMVKDRLLPFT 868
Cdd:cd18729    80 GGKRVVCYDDRFILKLAYESDGIVVSNDNYRDLQNEKPewKKFIEERLLMYS 131
KH-I_NYNRIN_like cd22477
type I K homology (KH) RNA-binding domain found in the subfamily of NYN domain and retroviral ...
 75-140 1.51e-35

type I K homology (KH) RNA-binding domain found in the subfamily of NYN domain and retroviral integrase catalytic domain-containing protein (NYNRIN); The NYNRIN subfamily includes NYNRIN and KH and NYN domain-containing protein (KHNYN). NYNRIN, also known as CGIN1/Cousin of GIN1, may contribute to retroviral resistance in mammals by regulating the ubiquitination of viral proteins. KHNYN acts as a novel cofactor for zinc finger antiviral protein (ZAP) to target CpG-containing retroviral RNA for degradation.


Pssm-ID: 411905  Cd Length: 66  Bit Score: 129.83  E-value: 1.51e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 256220954   75 PELWKEVRYPPVLHCAFLGAQGLFLDCLCWSTLAYLVPGPPGSLMVGGLTESFTMTQNWLEELVAR 140
Cdd:cd22477     1 PELTKEVLYPRDLHCIFLGAKGLFLDCLIWGTSAHIVPGAPGSLLISGLTEAFVMAQSRIEDLVEK 66
KH-I_N4BP1_like_rpt2 cd22388
second type I K homology (KH) RNA-binding domain found in the family of NEDD4-binding protein ...
 76-138 5.61e-33

second type I K homology (KH) RNA-binding domain found in the family of NEDD4-binding protein 1 (N4BP1); The N4BP1 family includes N4BP1, NYN domain and retroviral integrase catalytic domain-containing protein (NYNRIN) and KH and NYN domain-containing protein (KHNYN). These proteins are probably of retroviral origin. N4BP1 interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally downregulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. N4BP1 acts by interacting with the second WW domain of ITCH, leading to compete with ITCH's substrates and impairing ubiquitination of substrates. NYNRIN, also known as CGIN1/Cousin of GIN1, may contribute to retroviral resistance in mammals by regulating the ubiquitination of viral proteins. KHNYN acts as a novel cofactor for zinc finger antiviral protein (ZAP) to target CpG-containing retroviral RNA for degradation. Members of this family contains two type I K homology (KH) RNA-binding domain. The model corresponds to the second one.


Pssm-ID: 411816  Cd Length: 63  Bit Score: 122.27  E-value: 5.61e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 256220954   76 ELWKEVRYPPVLHCAFLGAQGLFLDCLCWSTLAYLVPGPPGSLMVGGLTESFTMTQNWLEELV 138
Cdd:cd22388     1 ELWKEVRYPKDMHCIFLGAQGLFLDSLIWSTLAYLVPGPPGSLMIGGLTESVVMAQSWIQEFV 63
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1073-1173 6.52e-20

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 86.40  E-value: 6.52e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954  1073 WNQEHEKSFLALKRALVCALCLSTPNPNLPFYLEVTVSQVSLTASLHQEHS-GRKHPIAYTSKPLLPDE------DSEGp 1145
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdGGERPIAYASRKLSPAErnysttEKEL- 79

                           90       100
                   ....*....|....*....|....*...
gi 256220954  1146 qsggdspYAVAWALKHFARCVGDNPVVL 1173
Cdd:pfam17919   80 -------LAIVFALKKFRHYLLGRKFTV 100
KH-I_N4BP1_like_rpt1 cd09032
first type I K homology (KH) RNA-binding domain found in the family of NEDD4-binding protein 1 ...
 12-73 7.59e-19

first type I K homology (KH) RNA-binding domain found in the family of NEDD4-binding protein 1 (N4BP1); The N4BP1 family includes N4BP1, NYN domain and retroviral integrase catalytic domain-containing protein (NYNRIN) and KH and NYN domain-containing protein (KHNYN). These proteins are probably of retroviral origin. N4BP1 interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally downregulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. N4BP1 acts by interacting with the second WW domain of ITCH, leading to compete with ITCH's substrates and impairing ubiquitination of substrates. NYNRIN, also known as CGIN1/Cousin of GIN1, may contribute to retroviral resistance in mammals by regulating the ubiquitination of viral proteins. KHNYN acts as a novel cofactor for zinc finger antiviral protein (ZAP) to target CpG-containing retroviral RNA for degradation. Members of this family contains two type I K homology (KH) RNA-binding domain. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411808  Cd Length: 65  Bit Score: 81.95  E-value: 7.59e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 256220954   12 EWFMVQTKSKPRVHRQRLQVQRIFRVKVT---AFQSRPDTPYFWLQLEGPRENTGKAKEYLKGLC 73
Cdd:cd09032     1 DEFVVPAEKVPLLERSRPRIERLFGVKVSlleELSKPKDGGKQWVQLEGDEEDVRKAKEYIKALC 65
PIN_PRORP-Zc3h12a-like cd18671
PIN domain of protein-only RNase P (PRORP), ribonuclease Zc3h12a, and related proteins; PRORPs ...
 743-847 2.51e-17

PIN domain of protein-only RNase P (PRORP), ribonuclease Zc3h12a, and related proteins; PRORPs catalyze the maturation of the 5' end of precursor tRNAs in eukaryotes. This family includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3, PRORP1 localizes to the chloroplast and the mitochondria, and PRORP2 and PRORP3 localize to the nucleus. Zc3h12a (zinc finger CCCH-type containing 12A, also known as MCPIP1/MCP induced protein 1 and Regnase-1) is a critical regulator of inflammatory response, with additional roles in defense against viruses and various stresses, cellular differentiation, and apoptosis. This PIN_PRORP-Zc3h12a-like family also includes Caenorhabditis elegans REGE-1 (REGnasE-1), which also functions as a cytoplasmic endonuclease. Additionally, it includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4, as well as N4BP1 (NEDD4-binding partner-1), NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350238  Cd Length: 126  Bit Score: 79.99  E-value: 2.51e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954  743 VVIDGSSVAMVHGLQHFFSCRGIAMAVQYFWNRGH--REITVFVPTWQLKKNRRV--RESHFLTKLHRLKMLSITPSqle 818
Cdd:cd18671     1 AVIDGANVGLSHQNKESFSCRQLLLAVNWFLERSHnnTDPLVFLHKWRVEQPRPVppTDRHLLEEWEKKGILYATPP--- 77

                          90       100
                  ....*....|....*....|....*....
gi 256220954  819 ngkkiTTYDYRFMVKLAEETDGVIVTNEQ 847
Cdd:cd18671    78 -----GSNDDWYWLYAAYESKCLLVTNDE 101
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1479-1532 1.96e-14

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 69.20  E-value: 1.96e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 256220954  1479 VPRQLRRDLIFSVHDSpiGEHQGLEDTYKTVRLLGWWPGMQDHVRDYCRSCLFC 1532
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETC 52
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1098-1207 2.31e-09

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 56.36  E-value: 2.31e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954  1098 NPNLPFYLEVTVSQVSLTASLHQ-EHSGRKHPIAYTSKPLLPDE------DSEGpqsggdspYAVAWALKHFARCVGDNP 1170
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQkDEDGKERPIAYASRKLTPAErnysttEKEL--------LAIVWALKKFRHYLLGRK 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 256220954  1171 VVLrlsyasRTtvDNEA---WDSRRASKAWLIRWSLLLQD 1207
Cdd:pfam17917   73 FTV------YT--DHKPlkyLFTPKELNGRLARWALFLQE 104
KH-I_N4BP1 cd22476
type I K homology (KH) RNA-binding domain found in NEDD4-binding protein 1 (N4BP1) and similar ...
 75-139 1.34e-07

type I K homology (KH) RNA-binding domain found in NEDD4-binding protein 1 (N4BP1) and similar proteins; N4BP1 interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally downregulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. N4BP1 acts by interacting with the second WW domain of ITCH, leading to compete with ITCH's substrates and impairing ubiquitination of substrates.


Pssm-ID: 411904  Cd Length: 68  Bit Score: 50.12  E-value: 1.34e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 256220954   75 PELWKEVRYPPVLHCAFLGAQGLFLDCLCWSTLAYLVPGPPGSLMVGGLTESFTMTQNWLEELVA 139
Cdd:cd22476     1 PELEEKEYYPKDMHCIFAGAQGLFLNSLIQDTCADVSVLDIGVLGIKGGAEAVVMAQSRIQQFVK 65
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1104-1207 6.89e-05

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 44.02  E-value: 6.89e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256220954 1104 YLEVTVSQVSLTASLHQEHS-GRKHPIAYTSKPLLPDE------DSEGpqsggdspYAVAWALKHFARCVGDNPVVLRls 1176
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDdGKERPIAFFSRKLTPAErnysttEKEL--------LAIVWALKKFRHYLLGRPFTVY-- 70

                          90       100       110
                  ....*....|....*....|....*....|....
gi 256220954 1177 yasrttVDNEA---WDSRRASKAWLIRWSLLLQD 1207
Cdd:cd09274    71 ------TDHKAlkyLLTQKDLNGRLARWLLLLSE 98
 
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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