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Conserved domains on  [gi|1021311939|ref|NP_001310545|]
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nonsense-mediated mRNA decay factor SMG5 isoform 4 [Homo sapiens]

Protein Classification

EST1_DNA_bind and PIN_Smg5 domain-containing protein( domain architecture ID 12105295)

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 ...
 789-947 1.64e-74

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: 241.41  E-value: 1.64e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 789 PYLVPDTQALCHHLPVIRQLATSGRFIVIIPRTVIDGLDLLKKEHPGARDGIRYLEAEFKKGNRYIRCQKEVGKSfERHK 868
Cdd:cd09884     1 PYLVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKKESAGAREAIRWLEAEFKKGNRYIRAQKPNEKL-PLPL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 869 LKRQ---DADAWTLYKILDSCKQLTLAQGAGEEDPSGMVTIITGLPLDNPSvLSGPMQAALQAAAHASVDIKNVLDFYKQ 945
Cdd:cd09884    80 LKRPkkkDRDAWRLYQILDCCKYLAQQQGDGEEDGAGMVTLLTGNDLDEKE-AFNKGFSVLGAAHAAGVEIENILDFYSK 158


                  ..
gi 1021311939 946 WK 947
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 ...
 131-344 3.17e-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: 3.17e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 131 AERFYYQALSVAPQIGMPFNQLGTLAGSKYYNVEAMYCYLRCIQSEVSFEGAYGNLKRLYDKAAKMYHQLKKCETRKLSP 210
Cdd:pfam10373   1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKLSPESLQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 211 GKKRCKDIKRLLVNFMYLQS-LLQPKSSSVDSEltsLCQSVLEDFNLCLFYLPSSPNlslasedeeeyesgyaFLPDLLI 289
Cdd:pfam10373  81 EGTPGDLLERLISLFLYLHGkLYTPTDFSEFPE---LEDEVLKKLEILLKESLLSRY----------------LKSRSLL 141

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1021311939 290 FQMVIICLMCVHSLERAGSKQY------SAAIAFTLALFSHLVNHVNirlQAELEEGENPV 344
Cdd:pfam10373 142 LKMLLINIFAFENAKDKSSPEEtkqfllRLALRFFFTLFGLLLEEVN---TLEALKSFTPV 199
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 11-122 4.13e-18

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: 80.43  E-value: 4.13e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939  11 KAEELLWRKVYYEVIQLIKTNKKHIHS----------RSTLECAYRTHLVAGIGFYQHLLLYIQSHyqlelqccidwthv 80
Cdd:pfam10374   1 KVLDLLWRKTHYPIIKWFRKWRKRLDGnskkkkypveFRKLNSKLRKFLKSAQKFYYGLIQRLVSR-------------- 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1021311939  81 tdpligckkpvSASGKEMDWAQMACHRCLVYLGDLSRYQNEL 122
Cdd:pfam10374  67 -----------EASSSLTALALLSCHRCLIYLGDLHRYRELL 97
 
Name Accession Description Interval E-value
PIN_Smg5-like cd09884
VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar ...
 789-947 1.64e-74

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: 241.41  E-value: 1.64e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 789 PYLVPDTQALCHHLPVIRQLATSGRFIVIIPRTVIDGLDLLKKEHPGARDGIRYLEAEFKKGNRYIRCQKEVGKSfERHK 868
Cdd:cd09884     1 PYLVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKKESAGAREAIRWLEAEFKKGNRYIRAQKPNEKL-PLPL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 869 LKRQ---DADAWTLYKILDSCKQLTLAQGAGEEDPSGMVTIITGLPLDNPSvLSGPMQAALQAAAHASVDIKNVLDFYKQ 945
Cdd:cd09884    80 LKRPkkkDRDAWRLYQILDCCKYLAQQQGDGEEDGAGMVTLLTGNDLDEKE-AFNKGFSVLGAAHAAGVEIENILDFYSK 158


                  ..
gi 1021311939 946 WK 947
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 ...
 131-344 3.17e-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: 3.17e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 131 AERFYYQALSVAPQIGMPFNQLGTLAGSKYYNVEAMYCYLRCIQSEVSFEGAYGNLKRLYDKAAKMYHQLKKCETRKLSP 210
Cdd:pfam10373   1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKLSPESLQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 211 GKKRCKDIKRLLVNFMYLQS-LLQPKSSSVDSEltsLCQSVLEDFNLCLFYLPSSPNlslasedeeeyesgyaFLPDLLI 289
Cdd:pfam10373  81 EGTPGDLLERLISLFLYLHGkLYTPTDFSEFPE---LEDEVLKKLEILLKESLLSRY----------------LKSRSLL 141

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1021311939 290 FQMVIICLMCVHSLERAGSKQY------SAAIAFTLALFSHLVNHVNirlQAELEEGENPV 344
Cdd:pfam10373 142 LKMLLINIFAFENAKDKSSPEEtkqfllRLALRFFFTLFGLLLEEVN---TLEALKSFTPV 199
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 11-122 4.13e-18

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: 80.43  E-value: 4.13e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939  11 KAEELLWRKVYYEVIQLIKTNKKHIHS----------RSTLECAYRTHLVAGIGFYQHLLLYIQSHyqlelqccidwthv 80
Cdd:pfam10374   1 KVLDLLWRKTHYPIIKWFRKWRKRLDGnskkkkypveFRKLNSKLRKFLKSAQKFYYGLIQRLVSR-------------- 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1021311939  81 tdpligckkpvSASGKEMDWAQMACHRCLVYLGDLSRYQNEL 122
Cdd:pfam10374  67 -----------EASSSLTALALLSCHRCLIYLGDLHRYRELL 97
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 790-889 4.66e-10

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: 57.82  E-value: 4.66e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939  790 YLVPDTQALCHHL--PVIRQLAtSGRFIVIIPRTVIDGLDLLKkehpgaRDGIRYLEAEFKKGNRYIRCQKEVGksFERH 867
Cdd:smart00670   2 KVVLDTNVLIDGLirDALEKLL-EKKGEVYIPQTVLEELEYLA------LRSLKKLEELALEGKIILKVLKEER--IEEE 72

                           90       100
                   ....*....|....*....|....*
gi 1021311939  868 KLKRQDADAWTLY---KILDSCKQL 889
Cdd:smart00670  73 ILERLSLKLELLPndaLILATAKEL 97
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 791-889 4.65e-07

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: 49.92  E-value: 4.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 791 LVPDTQALCHHLPVIRQLatSGRFIVIIPRTVIDGLDLLKKEHPG--------ARDGIRYLEAEFKKGNRYIRCQKEVGK 862
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNF--GEENDVVIPITVLEELDGLKKGSDEsgrelarlARQANRWLDELLENNGGRLRGQTLDER 78

                          90       100
                  ....*....|....*....|....*..
gi 1021311939 863 SFERHKLKRQDAdawtlykILDSCKQL 889
Cdd:pfam13638  79 LPPDPFDKNDNR-------ILAVALYL 98
 
Name Accession Description Interval E-value
PIN_Smg5-like cd09884
VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar ...
 789-947 1.64e-74

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: 241.41  E-value: 1.64e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 789 PYLVPDTQALCHHLPVIRQLATSGRFIVIIPRTVIDGLDLLKKEHPGARDGIRYLEAEFKKGNRYIRCQKEVGKSfERHK 868
Cdd:cd09884     1 PYLVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKKESAGAREAIRWLEAEFKKGNRYIRAQKPNEKL-PLPL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 869 LKRQ---DADAWTLYKILDSCKQLTLAQGAGEEDPSGMVTIITGLPLDNPSvLSGPMQAALQAAAHASVDIKNVLDFYKQ 945
Cdd:cd09884    80 LKRPkkkDRDAWRLYQILDCCKYLAQQQGDGEEDGAGMVTLLTGNDLDEKE-AFNKGFSVLGAAHAAGVEIENILDFYSK 158


                  ..
gi 1021311939 946 WK 947
Cdd:cd09884   159 WK 160
PIN_Smg5-6-like cd09880
VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related ...
 792-909 1.94e-29

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: 114.70  E-value: 1.94e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 792 VPDTQALCHHLPVIRQLATSGRFIVIIPRTVIDGLDLLKKE----HPGARDGIRYLEAEFKKGNRYIRCQKEVGKSFERH 867
Cdd:cd09880     1 VFDTNILLSHLDVLKLLVESGKWTVVIPLIVITELDGLKKNpdplGPKARSALRYIEACLKKHSRWLRVQTSKGNYLADL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1021311939 868 K-----------LKRQDADAWTLYKILDSCKQLTLAqgageEDPSGMVTIITG 909
Cdd:cd09880    81 TirseqlsdaseLRRRNNDDRILECALWQQKHFVDR-----EDGDGKVVLVTN 128
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 131-344 3.17e-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: 3.17e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 131 AERFYYQALSVAPQIGMPFNQLGTLAGSKYYNVEAMYCYLRCIQSEVSFEGAYGNLKRLYDKAAKMYHQLKKCETRKLSP 210
Cdd:pfam10373   1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKLSPESLQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 211 GKKRCKDIKRLLVNFMYLQS-LLQPKSSSVDSEltsLCQSVLEDFNLCLFYLPSSPNlslasedeeeyesgyaFLPDLLI 289
Cdd:pfam10373  81 EGTPGDLLERLISLFLYLHGkLYTPTDFSEFPE---LEDEVLKKLEILLKESLLSRY----------------LKSRSLL 141

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1021311939 290 FQMVIICLMCVHSLERAGSKQY------SAAIAFTLALFSHLVNHVNirlQAELEEGENPV 344
Cdd:pfam10373 142 LKMLLINIFAFENAKDKSSPEEtkqfllRLALRFFFTLFGLLLEEVN---TLEALKSFTPV 199
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 11-122 4.13e-18

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: 80.43  E-value: 4.13e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939  11 KAEELLWRKVYYEVIQLIKTNKKHIHS----------RSTLECAYRTHLVAGIGFYQHLLLYIQSHyqlelqccidwthv 80
Cdd:pfam10374   1 KVLDLLWRKTHYPIIKWFRKWRKRLDGnskkkkypveFRKLNSKLRKFLKSAQKFYYGLIQRLVSR-------------- 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1021311939  81 tdpligckkpvSASGKEMDWAQMACHRCLVYLGDLSRYQNEL 122
Cdd:pfam10374  67 -----------EASSSLTALALLSCHRCLIYLGDLHRYRELL 97
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 790-889 4.86e-14

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: 71.14  E-value: 4.86e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 790 YLVPDTQALCHHLPVIRQLATSGRFIVIIPRTVIDGLDLLKKEHP---------------GARDGIRYLEAEFKKGNRYI 854
Cdd:cd09885     7 YLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSEsdsyadeahaeevqaKARKAVKFLEEQFEARNPYV 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1021311939 855 RCQKEVGKSFERHKLKRQDaDAWTLY-----KILDSCKQL 889
Cdd:cd09885    87 RALTSKGTLLDTIAFRSED-INDGDGgnnddLILSCCLNL 125
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 792-889 8.65e-11

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: 60.65  E-value: 8.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 792 VPDTQALCHHLPVIRQLA-----TSGRFIVIIPRTVIDGLDLLKKEHPG------ARDGIRYLEAEFKKGNRYIRCQK-- 858
Cdd:cd18727     1 VLDTNVLISHLDLLKQLVedvekLSLPVVIVIPWVVLQELDGLKKSKRKsslgwlARRASTWLLEKLRSKHPRVRGQAls 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1021311939 859 EVgksFERHKLKRQDADawtlYKILDSCKQL 889
Cdd:cd18727    81 ET---LRASGDPGESND----DAILDCCLYF 104
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 790-889 4.66e-10

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: 57.82  E-value: 4.66e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939  790 YLVPDTQALCHHL--PVIRQLAtSGRFIVIIPRTVIDGLDLLKkehpgaRDGIRYLEAEFKKGNRYIRCQKEVGksFERH 867
Cdd:smart00670   2 KVVLDTNVLIDGLirDALEKLL-EKKGEVYIPQTVLEELEYLA------LRSLKKLEELALEGKIILKVLKEER--IEEE 72

                           90       100
                   ....*....|....*....|....*
gi 1021311939  868 KLKRQDADAWTLY---KILDSCKQL 889
Cdd:smart00670  73 ILERLSLKLELLPndaLILATAKEL 97
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 791-889 4.65e-07

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: 49.92  E-value: 4.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311939 791 LVPDTQALCHHLPVIRQLatSGRFIVIIPRTVIDGLDLLKKEHPG--------ARDGIRYLEAEFKKGNRYIRCQKEVGK 862
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNF--GEENDVVIPITVLEELDGLKKGSDEsgrelarlARQANRWLDELLENNGGRLRGQTLDER 78

                          90       100
                  ....*....|....*....|....*..
gi 1021311939 863 SFERHKLKRQDAdawtlykILDSCKQL 889
Cdd:pfam13638  79 LPPDPFDKNDNR-------ILAVALYL 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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