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Conserved domains on  [gi|568922508|ref|XP_006501406|]
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nonsense-mediated mRNA decay factor SMG5 isoform X1 [Mus musculus]

Protein Classification

EST1_DNA_bind and PIN_Smg5 domain-containing protein( domain architecture ID 12105370)

protein containing domains EST1, EST1_DNA_bind, and PIN_Smg5

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_Smg5-like cd09884
VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar ...
 842-1000 2.50e-72

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: 236.02  E-value: 2.50e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508  842 PYLIPDTQALCYHLPLIRQLATSGRFIIIIPRTVIDGLDLLKKEQPGARDGIRYLEAEFKKGNRYIRCQKEVGKSfERHK 921
Cdd:cd09884     1 PYLVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKKESAGAREAIRWLEAEFKKGNRYIRAQKPNEKL-PLPL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508  922 LKRQ---DADAWTLYKILDSCRQLTLAQGAGEEDPSGMVTIITGLHLDSPSALSgPMQAALQAAAHASVDVKNVLDFYRQ 998
Cdd:cd09884    80 LKRPkkkDRDAWRLYQILDCCKYLAQQQGDGEEDGAGMVTLLTGNDLDEKEAFN-KGFSVLGAAHAAGVEIENILDFYSK 158


                  ..
gi 568922508  999 WK 1000
Cdd:cd09884   159 WK 160
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 183-397 2.92e-29

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: 118.28  E-value: 2.92e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   183 AERFYYQALSVAPQIGMPFNQLGTLAGSKYYNVEAMYCYLRCIQSEVSFEGAYGNLKRLYDKAAKMYHQLKKSETRKLSP 262
Cdd:pfam10373    1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKLSPESLQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   263 SKKRCKDIKRLLVNFMYLQS-LLQPKSSSVDSEltsLCQSVLEDFNLCLFYLPSSPNlgltnedeeecesgyaFLPDLLI 341
Cdd:pfam10373   81 EGTPGDLLERLISLFLYLHGkLYTPTDFSEFPE---LEDEVLKKLEILLKESLLSRY----------------LKSRSLL 141

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568922508   342 FQMAIICLMGVHSLKRAGS------KHYSAAIAFTLALFSHLINHVNirlQAELEEGENPVS 397
Cdd:pfam10373  142 LKMLLINIFAFENAKDKSSpeetkqFLLRLALRFFFTLFGLLLEEVN---TLEALKSFTPVA 200
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 77-174 1.10e-11

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: 61.94  E-value: 1.10e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508    77 KAEELLWRK------------------------HIHSRSTLECAYRTHLVAGIGFYQHLLLYIQSHyqlelqccidwthv 132
Cdd:pfam10374    1 KVLDLLWRKthypiikwfrkwrkrldgnskkkkYPVEFRKLNSKLRKFLKSAQKFYYGLIQRLVSR-------------- 66

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 568922508   133 tdplmgfkkpvSASGKEMDWAQMACHRCLVYLGDLSRYQNEL 174
Cdd:pfam10374   67 -----------EASSSLTALALLSCHRCLIYLGDLHRYRELL 97
EST1_DNA_bind super family cl26538
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 638-731 5.50e-03

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.


The actual alignment was detected with superfamily member pfam10373:

Pssm-ID: 431239  Cd Length: 279  Bit Score: 40.09  E-value: 5.50e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   638 AEGLLPAVKVFLDWLRTNPDLiIVCAQSSQSLWNRLSVLLNLLPASAELqdsglalcsevQGLLEGCELPDlpASLLLPE 717
Cdd:pfam10373  200 ATRYLPALRVYLCWLKSNPSV-LEFEDKDEKLVDSLSDLWNELLSSTLL-----------NSSFDVEKRPK--RDYLLEE 265

                           90
                   ....*....|....
gi 568922508   718 DMALRNLPPLRAAH 731
Cdd:pfam10373  266 DVELKGFSPLGYRL 279
 
Name Accession Description Interval E-value
PIN_Smg5-like cd09884
VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar ...
 842-1000 2.50e-72

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: 236.02  E-value: 2.50e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508  842 PYLIPDTQALCYHLPLIRQLATSGRFIIIIPRTVIDGLDLLKKEQPGARDGIRYLEAEFKKGNRYIRCQKEVGKSfERHK 921
Cdd:cd09884     1 PYLVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKKESAGAREAIRWLEAEFKKGNRYIRAQKPNEKL-PLPL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508  922 LKRQ---DADAWTLYKILDSCRQLTLAQGAGEEDPSGMVTIITGLHLDSPSALSgPMQAALQAAAHASVDVKNVLDFYRQ 998
Cdd:cd09884    80 LKRPkkkDRDAWRLYQILDCCKYLAQQQGDGEEDGAGMVTLLTGNDLDEKEAFN-KGFSVLGAAHAAGVEIENILDFYSK 158


                  ..
gi 568922508  999 WK 1000
Cdd:cd09884   159 WK 160
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 183-397 2.92e-29

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: 118.28  E-value: 2.92e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   183 AERFYYQALSVAPQIGMPFNQLGTLAGSKYYNVEAMYCYLRCIQSEVSFEGAYGNLKRLYDKAAKMYHQLKKSETRKLSP 262
Cdd:pfam10373    1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKLSPESLQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   263 SKKRCKDIKRLLVNFMYLQS-LLQPKSSSVDSEltsLCQSVLEDFNLCLFYLPSSPNlgltnedeeecesgyaFLPDLLI 341
Cdd:pfam10373   81 EGTPGDLLERLISLFLYLHGkLYTPTDFSEFPE---LEDEVLKKLEILLKESLLSRY----------------LKSRSLL 141

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568922508   342 FQMAIICLMGVHSLKRAGS------KHYSAAIAFTLALFSHLINHVNirlQAELEEGENPVS 397
Cdd:pfam10373  142 LKMLLINIFAFENAKDKSSpeetkqFLLRLALRFFFTLFGLLLEEVN---TLEALKSFTPVA 200
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 77-174 1.10e-11

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: 61.94  E-value: 1.10e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508    77 KAEELLWRK------------------------HIHSRSTLECAYRTHLVAGIGFYQHLLLYIQSHyqlelqccidwthv 132
Cdd:pfam10374    1 KVLDLLWRKthypiikwfrkwrkrldgnskkkkYPVEFRKLNSKLRKFLKSAQKFYYGLIQRLVSR-------------- 66

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 568922508   133 tdplmgfkkpvSASGKEMDWAQMACHRCLVYLGDLSRYQNEL 174
Cdd:pfam10374   67 -----------EASSSLTALALLSCHRCLIYLGDLHRYRELL 97
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 843-942 1.91e-09

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: 56.28  E-value: 1.91e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508    843 YLIPDTQALCYHL--PLIRQLAtSGRFIIIIPRTVIDGLDLLKkeqpgaRDGIRYLEAEFKKGNRYIRCQKEVGksFERH 920
Cdd:smart00670    2 KVVLDTNVLIDGLirDALEKLL-EKKGEVYIPQTVLEELEYLA------LRSLKKLEELALEGKIILKVLKEER--IEEE 72

                            90       100
                    ....*....|....*....|....*
gi 568922508    921 KLKRQDADAWTLY---KILDSCRQL 942
Cdd:smart00670   73 ILERLSLKLELLPndaLILATAKEL 97
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 844-942 4.89e-06

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: 46.84  E-value: 4.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   844 LIPDTQALCYHLPLIRQLatSGRFIIIIPRTVIDGLDLLKKEQPG--------ARDGIRYLEAEFKKGNRYIRCQKEVGK 915
Cdd:pfam13638    1 YVLDTNVLLHDPDALFNF--GEENDVVIPITVLEELDGLKKGSDEsgrelarlARQANRWLDELLENNGGRLRGQTLDER 78

                           90       100
                   ....*....|....*....|....*..
gi 568922508   916 SFERHKLKRQDAdawtlykILDSCRQL 942
Cdd:pfam13638   79 LPPDPFDKNDNR-------ILAVALYL 98
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 638-731 5.50e-03

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: 40.09  E-value: 5.50e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   638 AEGLLPAVKVFLDWLRTNPDLiIVCAQSSQSLWNRLSVLLNLLPASAELqdsglalcsevQGLLEGCELPDlpASLLLPE 717
Cdd:pfam10373  200 ATRYLPALRVYLCWLKSNPSV-LEFEDKDEKLVDSLSDLWNELLSSTLL-----------NSSFDVEKRPK--RDYLLEE 265

                           90
                   ....*....|....
gi 568922508   718 DMALRNLPPLRAAH 731
Cdd:pfam10373  266 DVELKGFSPLGYRL 279
 
Name Accession Description Interval E-value
PIN_Smg5-like cd09884
VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar ...
 842-1000 2.50e-72

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: 236.02  E-value: 2.50e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508  842 PYLIPDTQALCYHLPLIRQLATSGRFIIIIPRTVIDGLDLLKKEQPGARDGIRYLEAEFKKGNRYIRCQKEVGKSfERHK 921
Cdd:cd09884     1 PYLVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKKESAGAREAIRWLEAEFKKGNRYIRAQKPNEKL-PLPL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508  922 LKRQ---DADAWTLYKILDSCRQLTLAQGAGEEDPSGMVTIITGLHLDSPSALSgPMQAALQAAAHASVDVKNVLDFYRQ 998
Cdd:cd09884    80 LKRPkkkDRDAWRLYQILDCCKYLAQQQGDGEEDGAGMVTLLTGNDLDEKEAFN-KGFSVLGAAHAAGVEIENILDFYSK 158


                  ..
gi 568922508  999 WK 1000
Cdd:cd09884   159 WK 160
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 183-397 2.92e-29

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: 118.28  E-value: 2.92e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   183 AERFYYQALSVAPQIGMPFNQLGTLAGSKYYNVEAMYCYLRCIQSEVSFEGAYGNLKRLYDKAAKMYHQLKKSETRKLSP 262
Cdd:pfam10373    1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKLSPESLQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   263 SKKRCKDIKRLLVNFMYLQS-LLQPKSSSVDSEltsLCQSVLEDFNLCLFYLPSSPNlgltnedeeecesgyaFLPDLLI 341
Cdd:pfam10373   81 EGTPGDLLERLISLFLYLHGkLYTPTDFSEFPE---LEDEVLKKLEILLKESLLSRY----------------LKSRSLL 141

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568922508   342 FQMAIICLMGVHSLKRAGS------KHYSAAIAFTLALFSHLINHVNirlQAELEEGENPVS 397
Cdd:pfam10373  142 LKMLLINIFAFENAKDKSSpeetkqFLLRLALRFFFTLFGLLLEEVN---TLEALKSFTPVA 200
PIN_Smg5-6-like cd09880
VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related ...
 845-962 2.51e-27

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: 108.53  E-value: 2.51e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508  845 IPDTQALCYHLPLIRQLATSGRFIIIIPRTVIDGLDLLKKEQ----PGARDGIRYLEAEFKKGNRYIRCQKEVGKSFERH 920
Cdd:cd09880     1 VFDTNILLSHLDVLKLLVESGKWTVVIPLIVITELDGLKKNPdplgPKARSALRYIEACLKKHSRWLRVQTSKGNYLADL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568922508  921 K-----------LKRQDADAWTLYKILDSCRQLTLAqgageEDPSGMVTIITG 962
Cdd:cd09880    81 TirseqlsdaseLRRRNNDDRILECALWQQKHFVDR-----EDGDGKVVLVTN 128
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 843-942 1.25e-13

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: 69.98  E-value: 1.25e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508  843 YLIPDTQALCYHLPLIRQLATSGRFIIIIPRTVIDGLDLLKKEQP---------------GARDGIRYLEAEFKKGNRYI 907
Cdd:cd09885     7 YLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSEsdsyadeahaeevqaKARKAVKFLEEQFEARNPYV 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 568922508  908 RCQKEVGKSFERHKLKRQDaDAWTLY-----KILDSCRQL 942
Cdd:cd09885    87 RALTSKGTLLDTIAFRSED-INDGDGgnnddLILSCCLNL 125
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 77-174 1.10e-11

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: 61.94  E-value: 1.10e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508    77 KAEELLWRK------------------------HIHSRSTLECAYRTHLVAGIGFYQHLLLYIQSHyqlelqccidwthv 132
Cdd:pfam10374    1 KVLDLLWRKthypiikwfrkwrkrldgnskkkkYPVEFRKLNSKLRKFLKSAQKFYYGLIQRLVSR-------------- 66

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 568922508   133 tdplmgfkkpvSASGKEMDWAQMACHRCLVYLGDLSRYQNEL 174
Cdd:pfam10374   67 -----------EASSSLTALALLSCHRCLIYLGDLHRYRELL 97
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 845-942 3.47e-10

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: 59.11  E-value: 3.47e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508  845 IPDTQALCYHLPLIRQLA-----TSGRFIIIIPRTVIDGLDLLKKEQPG------ARDGIRYLEAEFKKGNRYIRCQK-- 911
Cdd:cd18727     1 VLDTNVLISHLDLLKQLVedvekLSLPVVIVIPWVVLQELDGLKKSKRKsslgwlARRASTWLLEKLRSKHPRVRGQAls 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 568922508  912 EVgksFERHKLKRQDADawtlYKILDSCRQL 942
Cdd:cd18727    81 ET---LRASGDPGESND----DAILDCCLYF 104
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 843-942 1.91e-09

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: 56.28  E-value: 1.91e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508    843 YLIPDTQALCYHL--PLIRQLAtSGRFIIIIPRTVIDGLDLLKkeqpgaRDGIRYLEAEFKKGNRYIRCQKEVGksFERH 920
Cdd:smart00670    2 KVVLDTNVLIDGLirDALEKLL-EKKGEVYIPQTVLEELEYLA------LRSLKKLEELALEGKIILKVLKEER--IEEE 72

                            90       100
                    ....*....|....*....|....*
gi 568922508    921 KLKRQDADAWTLY---KILDSCRQL 942
Cdd:smart00670   73 ILERLSLKLELLPndaLILATAKEL 97
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 844-942 4.89e-06

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: 46.84  E-value: 4.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   844 LIPDTQALCYHLPLIRQLatSGRFIIIIPRTVIDGLDLLKKEQPG--------ARDGIRYLEAEFKKGNRYIRCQKEVGK 915
Cdd:pfam13638    1 YVLDTNVLLHDPDALFNF--GEENDVVIPITVLEELDGLKKGSDEsgrelarlARQANRWLDELLENNGGRLRGQTLDER 78

                           90       100
                   ....*....|....*....|....*..
gi 568922508   916 SFERHKLKRQDAdawtlykILDSCRQL 942
Cdd:pfam13638   79 LPPDPFDKNDNR-------ILAVALYL 98
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 638-731 5.50e-03

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: 40.09  E-value: 5.50e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568922508   638 AEGLLPAVKVFLDWLRTNPDLiIVCAQSSQSLWNRLSVLLNLLPASAELqdsglalcsevQGLLEGCELPDlpASLLLPE 717
Cdd:pfam10373  200 ATRYLPALRVYLCWLKSNPSV-LEFEDKDEKLVDSLSDLWNELLSSTLL-----------NSSFDVEKRPK--RDYLLEE 265

                           90
                   ....*....|....
gi 568922508   718 DMALRNLPPLRAAH 731
Cdd:pfam10373  266 DVELKGFSPLGYRL 279
 
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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