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Conserved domains on  [gi|37360070|dbj|BAC98013|]
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mKIAA0732 protein, partial [Mus musculus]

Protein Classification

telomerase-binding protein EST1A( domain architecture ID 12105297)

telomerase-binding protein EST1A is a component of the telomerase ribonucleoprotein (RNP) complex that is essential for the replication of chromosome termini

Gene Symbol:  SMG6
Gene Ontology:  GO:0004521|GO:0046872|GO:0043021|GO:0042162|GO:0032204

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 794-969 2.80e-96

VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs; Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN (PilT N terminus) domain elicits degradation of bound mRNAs, as well as, metal ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues) which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. Eukaryotic Smg6 PIN domains are present at the C-terminal end of the telomerase activating proteins, EST1.


:

Pssm-ID: 350233  Cd Length: 178  Bit Score: 300.72  E-value: 2.80e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 794 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLERRFE 872
Cdd:cd09885   1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 873 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDYMPTSKEEPIRLLREVVLLTDDRNLRVK 951
Cdd:cd09885  81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                       170
                ....*....|....*...
gi 37360070 952 ALTRNVPVRDIPAFLTWA 969
Cdd:cd09885 161 ALSRNIPVRDLPSFLKWA 178
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 304-656 1.44e-48

Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the site of polymerization. This is the DNA/RNA binding domain of EST1.


:

Pssm-ID: 431239  Cd Length: 279  Bit Score: 174.14  E-value: 1.44e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   304 ARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAEQMEKKQheefdm 383
Cdd:pfam10373   1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKL------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   384 SPDKWRKGkkstfrhvgddttrleiwihpshsrsaqgtesgkdseqenglgslSPSDLNKRFILSFLHAHGKLFTRIGME 463
Cdd:pfam10373  75 SPESLQEG---------------------------------------------TPGDLLERLISLFLYLHGKLYTPTDFS 109

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   464 TFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKDCfSEECRSVIQEQAASLGLAMFSLLVQRCT 540
Cdd:pfam10373 110 EFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDKSS-PEETKQFLLRLALRFFFTLFGLLLEEVN 188

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   541 CLLKDsakaqlsspedqedqddikvSSFVPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPLQVAVDVWSTLADFCNI 620
Cdd:pfam10373 189 TLEAL--------------------KSFTPVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLWNE 240

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 37360070   621 LTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 656
Cdd:pfam10373 241 LLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 191-296 2.81e-10

Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase at the site of polymerization. Structurally it resembles a TPR-like repeat.


:

Pssm-ID: 463062  Cd Length: 98  Bit Score: 58.09  E-value: 2.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   191 NVDQILWKNAFYQVIEKFRQLLK--DPNSENP------EQIRNRLLELLDEGSDFFDSLLQKLQvtykfKLEDymdglai 262
Cdd:pfam10374   1 KVLDLLWRKTHYPIIKWFRKWRKrlDGNSKKKkypvefRKLNSKLRKFLKSAQKFYYGLIQRLV-----SREA------- 68

                          90       100       110
                  ....*....|....*....|....*....|....
gi 37360070   263 rSKPLRKTVKYALisaQRSMICQGDISRYREQAN 296
Cdd:pfam10374  69 -SSSLTALALLSC---HRCLIYLGDLHRYRELLE 98
 
Name Accession Description Interval E-value
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 794-969 2.80e-96

VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs; Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN (PilT N terminus) domain elicits degradation of bound mRNAs, as well as, metal ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues) which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. Eukaryotic Smg6 PIN domains are present at the C-terminal end of the telomerase activating proteins, EST1.


Pssm-ID: 350233  Cd Length: 178  Bit Score: 300.72  E-value: 2.80e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 794 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLERRFE 872
Cdd:cd09885   1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 873 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDYMPTSKEEPIRLLREVVLLTDDRNLRVK 951
Cdd:cd09885  81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                       170
                ....*....|....*...
gi 37360070 952 ALTRNVPVRDIPAFLTWA 969
Cdd:cd09885 161 ALSRNIPVRDLPSFLKWA 178
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 304-656 1.44e-48

Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the site of polymerization. This is the DNA/RNA binding domain of EST1.


Pssm-ID: 431239  Cd Length: 279  Bit Score: 174.14  E-value: 1.44e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   304 ARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAEQMEKKQheefdm 383
Cdd:pfam10373   1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKL------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   384 SPDKWRKGkkstfrhvgddttrleiwihpshsrsaqgtesgkdseqenglgslSPSDLNKRFILSFLHAHGKLFTRIGME 463
Cdd:pfam10373  75 SPESLQEG---------------------------------------------TPGDLLERLISLFLYLHGKLYTPTDFS 109

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   464 TFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKDCfSEECRSVIQEQAASLGLAMFSLLVQRCT 540
Cdd:pfam10373 110 EFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDKSS-PEETKQFLLRLALRFFFTLFGLLLEEVN 188

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   541 CLLKDsakaqlsspedqedqddikvSSFVPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPLQVAVDVWSTLADFCNI 620
Cdd:pfam10373 189 TLEAL--------------------KSFTPVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLWNE 240

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 37360070   621 LTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 656
Cdd:pfam10373 241 LLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 801-961 2.16e-23

PIN domain; Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).


Pssm-ID: 433369  Cd Length: 131  Bit Score: 96.53  E-value: 2.16e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   801 LVPDTNGFIDHLASLARLLEsrKYILVVPLIVINELDGLAKGQETDHRaggyarVVQEKARKSIEFLERRFESRDSCLRA 880
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNFGE--ENDVVIPITVLEELDGLKKGSDESGR------ELARLARQANRWLDELLENNGGRLRG 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   881 LTSRGNELESIAFRseditgqlgnNDDLILSCCLHYckdkakdymptSKEEPIRllrEVVLLTDDRNLRVKALTRNVPVR 960
Cdd:pfam13638  73 QTLDERLPPDPFDK----------NDNRILAVALYL-----------KEELPDR---PVILVSKDINLRIKADALGIPAE 128


                  .
gi 37360070   961 D 961
Cdd:pfam13638 129 D 129
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 801-950 1.30e-12

Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.


Pssm-ID: 214771 [Multi-domain]  Cd Length: 111  Bit Score: 65.14  E-value: 1.30e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070    801 LVPDTNGFIDHLAS-LARLLESRKYILVVPLIVINELDGLAKgqetdHRAGGYARVVQEKARKSIEFLERRFESRdsclr 879
Cdd:smart00670   3 VVLDTNVLIDGLIRdALEKLLEKKGEVYIPQTVLEELEYLAL-----RSLKKLEELALEGKIILKVLKEERIEEE----- 72

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 37360070    880 altsrgnELESIAFRSEDITgqlgnNDDLILSCCLHYCKdkakdymptskeepirllreVVLLTDDRNLRV 950
Cdd:smart00670  73 -------ILERLSLKLELLP-----NDALILATAKELGN--------------------VVLVTNDRDLRR 111
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 191-296 2.81e-10

Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase at the site of polymerization. Structurally it resembles a TPR-like repeat.


Pssm-ID: 463062  Cd Length: 98  Bit Score: 58.09  E-value: 2.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   191 NVDQILWKNAFYQVIEKFRQLLK--DPNSENP------EQIRNRLLELLDEGSDFFDSLLQKLQvtykfKLEDymdglai 262
Cdd:pfam10374   1 KVLDLLWRKTHYPIIKWFRKWRKrlDGNSKKKkypvefRKLNSKLRKFLKSAQKFYYGLIQRLV-----SREA------- 68

                          90       100       110
                  ....*....|....*....|....*....|....
gi 37360070   263 rSKPLRKTVKYALisaQRSMICQGDISRYREQAN 296
Cdd:pfam10374  69 -SSSLTALALLSC---HRCLIYLGDLHRYRELLE 98
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
802-959 2.09e-07

rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 50.60  E-value: 2.09e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 802 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQetdhrAGGYARvvqeKARKSIEFLERrfesr 874
Cdd:COG1412   4 LLDTNALmmpaqfgVDVFEELDRLL--GKYEFIVPEAVLEELEKLSRGA-----KGKEKR----AARVALDLAER----- 67

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 875 dsclraltsrgnelesiaFRSEDITGqlGNNDDLILSCclhyckdkAKDYmptskeepirllrEVVLLTDDRNLRVKALT 954
Cdd:COG1412  68 ------------------CEIVETEG--GYADDAILEL--------AKEN-------------GVIVATNDKELRRRLLE 106


                ....*
gi 37360070 955 RNVPV 959
Cdd:COG1412 107 AGIPV 111
 
Name Accession Description Interval E-value
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 794-969 2.80e-96

VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs; Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN (PilT N terminus) domain elicits degradation of bound mRNAs, as well as, metal ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues) which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. Eukaryotic Smg6 PIN domains are present at the C-terminal end of the telomerase activating proteins, EST1.


Pssm-ID: 350233  Cd Length: 178  Bit Score: 300.72  E-value: 2.80e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 794 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLERRFE 872
Cdd:cd09885   1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 873 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDYMPTSKEEPIRLLREVVLLTDDRNLRVK 951
Cdd:cd09885  81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                       170
                ....*....|....*...
gi 37360070 952 ALTRNVPVRDIPAFLTWA 969
Cdd:cd09885 161 ALSRNIPVRDLPSFLKWA 178
PIN_Smg5-6-like cd09880
VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related ...
 802-968 2.44e-49

VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related proteins; PIN (PilT N terminus) domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and homologs are included in this family. Smg5 and Smg6 are essential factors in NMD, a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN domain elicits degradation of bound mRNAs, as well as, metal-ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. Many of the bacterial homologs in this group have an N-terminal PIN domain and a C-terminal PhoH-like ATPase domain.


Pssm-ID: 350228  Cd Length: 152  Bit Score: 171.32  E-value: 2.44e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 802 VPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETdhraggyarvVQEKARKSIEFLERRFESRDSCLRAL 881
Cdd:cd09880   1 VFDTNILLSHLDVLKLLVESGKWTVVIPLIVITELDGLKKNPDP----------LGPKARSALRYIEACLKKHSRWLRVQ 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 882 TSRGNELESIAFRSE----DITGQLGNNDDLILSCCLHYCKDKAKDYMPTSKeepirllreVVLLTDDRNLRVKALTRNV 957
Cdd:cd09880  71 TSKGNYLADLTIRSEqlsdASELRRRNNDDRILECALWQQKHFVDREDGDGK---------VVLVTNDRNLRLKARARGV 141

                       170
                ....*....|.
gi 37360070 958 PVRDIPAFLTW 968
Cdd:cd09880 142 EAVTVKELLKS 152
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 304-656 1.44e-48

Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the site of polymerization. This is the DNA/RNA binding domain of EST1.


Pssm-ID: 431239  Cd Length: 279  Bit Score: 174.14  E-value: 1.44e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   304 ARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAEQMEKKQheefdm 383
Cdd:pfam10373   1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKL------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   384 SPDKWRKGkkstfrhvgddttrleiwihpshsrsaqgtesgkdseqenglgslSPSDLNKRFILSFLHAHGKLFTRIGME 463
Cdd:pfam10373  75 SPESLQEG---------------------------------------------TPGDLLERLISLFLYLHGKLYTPTDFS 109

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   464 TFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKDCfSEECRSVIQEQAASLGLAMFSLLVQRCT 540
Cdd:pfam10373 110 EFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDKSS-PEETKQFLLRLALRFFFTLFGLLLEEVN 188

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   541 CLLKDsakaqlsspedqedqddikvSSFVPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPLQVAVDVWSTLADFCNI 620
Cdd:pfam10373 189 TLEAL--------------------KSFTPVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLWNE 240

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 37360070   621 LTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 656
Cdd:pfam10373 241 LLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 802-968 1.30e-26

VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; Saccharomyces cerevisiae mRNA-processing endoribonuclease Swt1p plays an important role in quality control of nuclear mRNPs in eukaryotes. Human transcriptional protein SWT1 (RNA endoribonuclease homolog, also known as HsSwt1, C1orf26, and chromosome 1 open reading frame 26) is an RNA endonuclease that participates in quality control of nuclear mRNPs and can associate with the nuclear pore complex (NPC). This subfamily belongs to the Smg5 and Smg6-like PIN domain family. Smg5 and Smg6 are essential factors in NMD, a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN domain elicits degradation of bound mRNAs, as well as, metal-ion dependent, degradation of single-stranded RNA, in vitro. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo.


Pssm-ID: 350294  Cd Length: 141  Bit Score: 106.10  E-value: 1.30e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 802 VPDTNGFIDHLASLARLLE-----SRKYILVVPLIVINELDGLAKGQETDHraggyarvVQEKARKSIEFLERRFESRDS 876
Cdd:cd18727   1 VLDTNVLISHLDLLKQLVEdveklSLPVVIVIPWVVLQELDGLKKSKRKSS--------LGWLARRASTWLLEKLRSKHP 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 877 CLRALTsrgnelesiafRSEDITGQ---LGNNDDLILSCCLHYCKdkakdymptskeepiRLLREVVLLTDDRNLRVKAL 953
Cdd:cd18727  73 RVRGQA-----------LSETLRASgdpGESNDDAILDCCLYFQE---------------KYGAPVVLLSNDKNLCNKAL 126

                       170
                ....*....|....*
gi 37360070 954 TRNVPVRDIPAFLTW 968
Cdd:cd18727 127 INGIPTISPEEGMTA 141
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 801-961 2.16e-23

PIN domain; Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).


Pssm-ID: 433369  Cd Length: 131  Bit Score: 96.53  E-value: 2.16e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   801 LVPDTNGFIDHLASLARLLEsrKYILVVPLIVINELDGLAKGQETDHRaggyarVVQEKARKSIEFLERRFESRDSCLRA 880
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNFGE--ENDVVIPITVLEELDGLKKGSDESGR------ELARLARQANRWLDELLENNGGRLRG 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   881 LTSRGNELESIAFRseditgqlgnNDDLILSCCLHYckdkakdymptSKEEPIRllrEVVLLTDDRNLRVKALTRNVPVR 960
Cdd:pfam13638  73 QTLDERLPPDPFDK----------NDNRILAVALYL-----------KEELPDR---PVILVSKDINLRIKADALGIPAE 128


                  .
gi 37360070   961 D 961
Cdd:pfam13638 129 D 129
PIN_VapC_PhoHL-ATPase cd09883
VapC-like PIN domain of bacterial Smg6-like proteins with C-terminal PhoH-like ATPase domains; ...
 802-961 1.14e-12

VapC-like PIN domain of bacterial Smg6-like proteins with C-terminal PhoH-like ATPase domains; PIN (PilT N terminus) domain of Smg6-like bacterial proteins with C-terminal PhoH-like ATPase domains and other similar homologs are included in this family. Eukaryotic Smg5 and Smg6 nucleases are essential factors in nonsense-mediated mRNA decay (NMD), a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN domain elicits degradation of bound mRNAs, as well as, metal ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues). Many of the bacterial homologs in this group have an N-terminal PIN domain and a C-terminal PhoH-like ATPase domain and are predicted to be ATPases which are induced by phosphate starvation.


Pssm-ID: 350231  Cd Length: 146  Bit Score: 66.41  E-value: 1.14e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 802 VPDTNGFI-DHLAslarLLESRKYILVVPLIVINELDGLAKGQETDHRAggyARVVQ---EKARKSIEFLERRFESRDSC 877
Cdd:cd09883   5 VLDTNVLLhDPNA----IFKFEDNDVVIPITVLEELDKLKKRNDELGRN---AREAIrnlDELREKGSLAEGVPLENGGT 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 878 LRALTSRGNELESIAFRseditgqLGNNDDLILSCCLHYCKDKAKDymptskeepirllreVVLLTDDRNLRVKALTRNV 957
Cdd:cd09883  78 LRVELNHKDLLPLPELD-------LDKNDNRILAVALKLKEEGDRP---------------VILVTKDINLRIKADALGI 135


                ....
gi 37360070 958 PVRD 961
Cdd:cd09883 136 KAED 139
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 801-950 1.30e-12

Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.


Pssm-ID: 214771 [Multi-domain]  Cd Length: 111  Bit Score: 65.14  E-value: 1.30e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070    801 LVPDTNGFIDHLAS-LARLLESRKYILVVPLIVINELDGLAKgqetdHRAGGYARVVQEKARKSIEFLERRFESRdsclr 879
Cdd:smart00670   3 VVLDTNVLIDGLIRdALEKLLEKKGEVYIPQTVLEELEYLAL-----RSLKKLEELALEGKIILKVLKEERIEEE----- 72

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 37360070    880 altsrgnELESIAFRSEDITgqlgnNDDLILSCCLHYCKdkakdymptskeepirllreVVLLTDDRNLRV 950
Cdd:smart00670  73 -------ILERLSLKLELLP-----NDALILATAKELGN--------------------VVLVTNDRDLRR 111
PIN_Smg5-like cd09884
VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar ...
 800-887 2.78e-10

VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs; Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo.


Pssm-ID: 350232  Cd Length: 160  Bit Score: 59.98  E-value: 2.78e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 800 FLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKgqetdhraggyarvVQEKARKSIEFLERRFESRDSCLR 879
Cdd:cd09884   2 YLVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKK--------------ESAGAREAIRWLEAEFKKGNRYIR 67


                ....*...
gi 37360070 880 ALtsRGNE 887
Cdd:cd09884  68 AQ--KPNE 73
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 191-296 2.81e-10

Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase at the site of polymerization. Structurally it resembles a TPR-like repeat.


Pssm-ID: 463062  Cd Length: 98  Bit Score: 58.09  E-value: 2.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070   191 NVDQILWKNAFYQVIEKFRQLLK--DPNSENP------EQIRNRLLELLDEGSDFFDSLLQKLQvtykfKLEDymdglai 262
Cdd:pfam10374   1 KVLDLLWRKTHYPIIKWFRKWRKrlDGNSKKKkypvefRKLNSKLRKFLKSAQKFYYGLIQRLV-----SREA------- 68

                          90       100       110
                  ....*....|....*....|....*....|....
gi 37360070   263 rSKPLRKTVKYALisaQRSMICQGDISRYREQAN 296
Cdd:pfam10374  69 -SSSLTALALLSC---HRCLIYLGDLHRYRELLE 98
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
802-959 2.09e-07

rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 50.60  E-value: 2.09e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 802 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQetdhrAGGYARvvqeKARKSIEFLERrfesr 874
Cdd:COG1412   4 LLDTNALmmpaqfgVDVFEELDRLL--GKYEFIVPEAVLEELEKLSRGA-----KGKEKR----AARVALDLAER----- 67

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 875 dsclraltsrgnelesiaFRSEDITGqlGNNDDLILSCclhyckdkAKDYmptskeepirllrEVVLLTDDRNLRVKALT 954
Cdd:COG1412  68 ------------------CEIVETEG--GYADDAILEL--------AKEN-------------GVIVATNDKELRRRLLE 106


                ....*
gi 37360070 955 RNVPV 959
Cdd:COG1412 107 AGIPV 111
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 802-960 6.37e-06

VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, rRNA-processing protein Fcf1, Archaeoglobus fulgidus AF0591 protein, and homologs; PIN (PilT N terminus) domains of such ribonucleases as the toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1, are included in VapC-like this family. Also included are the PIN domains of the Pyrobaculum aerophilum Pea0151 and Archaeoglobus fulgidus AF0591 proteins and other similar archaeal homologs. The PIN 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: 350205  Cd Length: 129  Bit Score: 46.50  E-value: 6.37e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 802 VPDTNGFIDHLAS------LARLLESR--KYILVVPLIVINELDGLAKGQETDHRAggyarvvqekarksieflERRFES 873
Cdd:cd09854   1 VLDTNVLIALLSSepeseaAKELLALLlgDSELVIPPLVLAELLRLLARERGARRA------------------LEILEL 62

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 874 RDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYckdkakdymptskeepirllREVVLLTDDRNLRvKAL 953
Cdd:cd09854  63 LRALEVVEEEPALAEIALEVLALGLERGLDFGDALILALAKEL--------------------GGAVLVTNDRDFR-RLA 121


                ....*..
gi 37360070 954 TRNVPVR 960
Cdd:cd09854 122 KLGLKVI 128
PIN_VapC_AF0591-like cd09879
VapC-like PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal ...
 802-959 6.46e-05

VapC-like PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal homologs; PIN (PilT N terminus) domain of Archaeoglobus fulgidus AF0591 protein and other similar uncharacterized archaeal homologs are included in this family. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) 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. Some members of the superfamily lack several of these key catalytic residues. PIN domains within this subgroup contain four of these highly conserved putative metal-binding, active site 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. Matelska et al. recently classified PIN-like domains and included distant subgroups, this subgroup includes some sequences belonging to one of these, PIN_14.


Pssm-ID: 350227 [Multi-domain]  Cd Length: 118  Bit Score: 43.22  E-value: 6.46e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 802 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQETDHRAggYARVvqekARKSIEflerRFESR 874
Cdd:cd09879   2 ILDTNFLmypfqfgVDIFEELERLL--GKYEIVVPSAVIEELERLAKKGKGKDKR--AARL----ALKLAE----RCKVV 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37360070 875 DsclraltsrgnelesiafrSEDITGqlgnnDDLILSCclhyckdkAKDYmptskeepirllrEVVLLTDDRNLRVKALT 954
Cdd:cd09879  70 E-------------------SEGEPA-----DDAILEL--------AKEL-------------GAIVATNDRELRKRLRE 104


                ....*
gi 37360070 955 RNVPV 959
Cdd:cd09879 105 KGIPV 109
 
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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