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Conserved domains on  [gi|2057765590|emb|CAB4406875|]
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unnamed protein product [Rhizophagus irregularis]

Protein Classification

EST1A family protein( domain architecture ID 12105294)

EST1A (ever shorter telomeres 1A) family protein similar to telomerase-binding protein EST1A and protein SMG5/EST1B

CATH:  3.40.50.1010
EC:  3.1.-.-
Gene Ontology:  GO:0003723|GO:0042162|GO:0032204
PubMed:  28508407|28575517

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_Smg5-6-like cd09880
VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related ...
 830-985 3.42e-60

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: 202.14  E-value: 3.42e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 830 IVDTNCLIGDLEIVKKVIQSEKWVVIVPSIVVTELDGLKYNPPPLGHAAHEALEYLNETLSTKK--IRIQTSKGNYLTDI 907
Cdd:cd09880     1 VFDTNILLSHLDVLKLLVESGKWTVVIPLIVITELDGLKKNPDPLGPKARSALRYIEACLKKHSrwLRVQTSKGNYLADL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2057765590 908 SFSEEFDFGNGEDKKKNLDDLILGICLWHSKHNEknglhdKSNENNEVTVLLTNDRNLRVKARARGVNVVGVKDFTGI 985
Cdd:cd09880    81 TIRSEQLSDASELRRRNNDDRILECALWQQKHFV------DREDGDGKVVLVTNDRNLRLKARARGVEAVTVKELLKS 152
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 327-640 1.42e-21

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: 95.94  E-value: 1.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 327 ASRWYRLGIHLNSNNGKFYHHLAILASQ--DELKALYYYCRSLMVNTPFMSTRESLVALFglDNMRQKPKGNRGYLQRDN 404
Cdd:pfam10373   1 ALRYYLLAILLLPSNGEPYNQLGVIALYvgNHLDAVYYFLRSLLSRNPFPTAKNNLELLF--DKIRSKLEQGELKLSPES 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 405 SKLKNYLDNQP-VENLFVRLHGMLFTKIGLEHFDETFQSFLDKlLKTNTFQRTSNSNRHWMEFYLFLAVINLSGLYNygn 483
Cdd:pfam10373  79 LQEGTPGDLLErLISLFLYLHGKLYTPTDFSEFPELEDEVLKK-LEILLKESLLSRYLKSRSLLLKMLLINIFAFEN--- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 484 enfiigkaqaakNKDDIQSLDADPIFAQES-RLTFIIMNHFMLKYLESEAYQPGHEVSEGWLLYCEIIMLWMVasgifdg 562
Cdd:pfam10373 155 ------------AKDKSSPEETKQFLLRLAlRFFFTLFGLLLEEVNTLEALKSFTPVATRYLPALRVYLCWLK------- 215

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2057765590 563 fangSNNSTWEKIMRKSDFpgsWEVFARFLTNithqIPSTTKEKILDSVNNDIEQESivqiqppALAEDWELRGISLL 640
Cdd:pfam10373 216 ----SNPSVLEFEDKDEKL---VDSLSDLWNE----LLSSTLLNSSFDVEKRPKRDY-------LLEEDVELKGFSPL 275
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 215-308 2.54e-07

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: 49.62  E-value: 2.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 215 DIESKCWKLGFYSLIEQFRSAVN-LDRRRSKNRITSSF-VISNQFSIFLDEAEIFYKRLLKHVAdgTKSIDKSIEKNKpp 292
Cdd:pfam10374   1 KVLDLLWRKTHYPIIKWFRKWRKrLDGNSKKKKYPVEFrKLNSKLRKFLKSAQKFYYGLIQRLV--SREASSSLTALA-- 76

                          90
                  ....*....|....*...
gi 2057765590 293 KWI--RCVCCLGDVTRYR 308
Cdd:pfam10374  77 LLSchRCLIYLGDLHRYR 94
 
Name Accession Description Interval E-value
PIN_Smg5-6-like cd09880
VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related ...
 830-985 3.42e-60

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: 202.14  E-value: 3.42e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 830 IVDTNCLIGDLEIVKKVIQSEKWVVIVPSIVVTELDGLKYNPPPLGHAAHEALEYLNETLSTKK--IRIQTSKGNYLTDI 907
Cdd:cd09880     1 VFDTNILLSHLDVLKLLVESGKWTVVIPLIVITELDGLKKNPDPLGPKARSALRYIEACLKKHSrwLRVQTSKGNYLADL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2057765590 908 SFSEEFDFGNGEDKKKNLDDLILGICLWHSKHNEknglhdKSNENNEVTVLLTNDRNLRVKARARGVNVVGVKDFTGI 985
Cdd:cd09880    81 TIRSEQLSDASELRRRNNDDRILECALWQQKHFV------DREDGDGKVVLVTNDRNLRLKARARGVEAVTVKELLKS 152
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 327-640 1.42e-21

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: 95.94  E-value: 1.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 327 ASRWYRLGIHLNSNNGKFYHHLAILASQ--DELKALYYYCRSLMVNTPFMSTRESLVALFglDNMRQKPKGNRGYLQRDN 404
Cdd:pfam10373   1 ALRYYLLAILLLPSNGEPYNQLGVIALYvgNHLDAVYYFLRSLLSRNPFPTAKNNLELLF--DKIRSKLEQGELKLSPES 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 405 SKLKNYLDNQP-VENLFVRLHGMLFTKIGLEHFDETFQSFLDKlLKTNTFQRTSNSNRHWMEFYLFLAVINLSGLYNygn 483
Cdd:pfam10373  79 LQEGTPGDLLErLISLFLYLHGKLYTPTDFSEFPELEDEVLKK-LEILLKESLLSRYLKSRSLLLKMLLINIFAFEN--- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 484 enfiigkaqaakNKDDIQSLDADPIFAQES-RLTFIIMNHFMLKYLESEAYQPGHEVSEGWLLYCEIIMLWMVasgifdg 562
Cdd:pfam10373 155 ------------AKDKSSPEETKQFLLRLAlRFFFTLFGLLLEEVNTLEALKSFTPVATRYLPALRVYLCWLK------- 215

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2057765590 563 fangSNNSTWEKIMRKSDFpgsWEVFARFLTNithqIPSTTKEKILDSVNNDIEQESivqiqppALAEDWELRGISLL 640
Cdd:pfam10373 216 ----SNPSVLEFEDKDEKL---VDSLSDLWNE----LLSSTLLNSSFDVEKRPKRDY-------LLEEDVELKGFSPL 275
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 829-980 3.53e-21

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: 90.37  E-value: 3.53e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 829 IIVDTNCLIGDLEIVKKViqSEKWVVIVPSIVVTELDGLKYNPPP----LGHAAHEALEYLNETL--STKKIRIQTSKGN 902
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNF--GEENDVVIPITVLEELDGLKKGSDEsgreLARLARQANRWLDELLenNGGRLRGQTLDER 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2057765590 903 YltdisfseefdfgNGEDKKKNlDDLILGICLWHSKHNEknglhdksnenNEVTVLLTNDRNLRVKARARGVNVVGVK 980
Cdd:pfam13638  79 L-------------PPDPFDKN-DNRILAVALYLKEELP-----------DRPVILVSKDINLRIKADALGIPAEDYE 131
YlaK COG1875
Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General ...
 830-976 3.30e-08

Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General function prediction only];


Pssm-ID: 441479 [Multi-domain]  Cd Length: 441  Bit Score: 57.02  E-value: 3.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 830 IVDTNCLIGDLEIVKKViqsEKWVVIVPSIVVTELDGLKYNPPPLGHAAHEALEYLNETLSTKKIR--IQTSKGNYLTDI 907
Cdd:COG1875     8 VLDTNVLLHDPNAIFRF---EEHDVVIPMVVLEELDKFKKGMSELGRNARQASRLLDELRAKGNLDegVPLPNGGTLRVE 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2057765590 908 SFSEEFDFGNGEDKKKNlDDLILGICLwhskhneknGLHDKSNENNevTVLLTNDRNLRVKARARGVNV 976
Cdd:COG1875    85 LNHKDSELPAGLPLDKN-DNRILAVAL---------NLQEEYPGRP--VILVSKDINLRIKADALGLEA 141
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 215-308 2.54e-07

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: 49.62  E-value: 2.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 215 DIESKCWKLGFYSLIEQFRSAVN-LDRRRSKNRITSSF-VISNQFSIFLDEAEIFYKRLLKHVAdgTKSIDKSIEKNKpp 292
Cdd:pfam10374   1 KVLDLLWRKTHYPIIKWFRKWRKrLDGNSKKKKYPVEFrKLNSKLRKFLKSAQKFYYGLIQRLV--SREASSSLTALA-- 76

                          90
                  ....*....|....*...
gi 2057765590 293 KWI--RCVCCLGDVTRYR 308
Cdd:pfam10374  77 LLSchRCLIYLGDLHRYR 94
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 829-967 2.10e-03

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: 38.94  E-value: 2.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590  829 IIVDTNCLIGDL--EIVKKVIQSEKwVVIVPSIVVTELDGLKYnppplghaahEALEYLNETLSTKKIRIQTSKGNyltd 906
Cdd:smart00670   3 VVLDTNVLIDGLirDALEKLLEKKG-EVYIPQTVLEELEYLAL----------RSLKKLEELALEGKIILKVLKEE---- 67

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2057765590  907 isFSEEFDFGNGEDKKKNL--DDLILGICLWHSKHneknglhdksnennevtVLLTNDRNLRV 967
Cdd:smart00670  68 --RIEEEILERLSLKLELLpnDALILATAKELGNV-----------------VLVTNDRDLRR 111
 
Name Accession Description Interval E-value
PIN_Smg5-6-like cd09880
VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related ...
 830-985 3.42e-60

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: 202.14  E-value: 3.42e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 830 IVDTNCLIGDLEIVKKVIQSEKWVVIVPSIVVTELDGLKYNPPPLGHAAHEALEYLNETLSTKK--IRIQTSKGNYLTDI 907
Cdd:cd09880     1 VFDTNILLSHLDVLKLLVESGKWTVVIPLIVITELDGLKKNPDPLGPKARSALRYIEACLKKHSrwLRVQTSKGNYLADL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2057765590 908 SFSEEFDFGNGEDKKKNLDDLILGICLWHSKHNEknglhdKSNENNEVTVLLTNDRNLRVKARARGVNVVGVKDFTGI 985
Cdd:cd09880    81 TIRSEQLSDASELRRRNNDDRILECALWQQKHFV------DREDGDGKVVLVTNDRNLRLKARARGVEAVTVKELLKS 152
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 822-983 8.58e-33

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: 125.06  E-value: 8.58e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 822 IVPGYtsIIVDTNCLIGDLEIVKKVIQSEKWVVIVPSIVVTELDGLK-----YNPPPLGHA------AHEALEYLNETLS 890
Cdd:cd09885     3 VRPRY--LVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAkgsesDSYADEAHAeevqakARKAVKFLEEQFE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 891 TK--KIRIQTSKGNYLTDISFSEEFDfgNGEDKKKNlDDLILGICLWHSKHNEKNGLHDKSNE----NNEVtVLLTNDRN 964
Cdd:cd09885    81 ARnpYVRALTSKGTLLDTIAFRSEDI--NDGDGGNN-DDLILSCCLNLCKDKAVDFMPASKDQpirlYREV-VLLTDDRN 156

                         170
                  ....*....|....*....
gi 2057765590 965 LRVKARARGVNVVGVKDFT 983
Cdd:cd09885   157 LRVKALSRNIPVRDLPSFL 175
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 830-982 5.61e-23

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: 95.70  E-value: 5.61e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 830 IVDTNCLIGDLEIVKKVIQSEKW-----VVIVPSIVVTELDGLKYNP--PPLGHAAHEALEYLNETLSTKK--IRIQTSK 900
Cdd:cd18727     1 VLDTNVLISHLDLLKQLVEDVEKlslpvVIVIPWVVLQELDGLKKSKrkSSLGWLARRASTWLLEKLRSKHprVRGQALS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 901 gnyltdisfseEFDFGNGEDKKKNlDDLILGICLWHSKHNEKNglhdksnennevTVLLTNDRNLRVKARARGVNVVGVK 980
Cdd:cd18727    81 -----------ETLRASGDPGESN-DDAILDCCLYFQEKYGAP------------VVLLSNDKNLCNKALINGIPTISPE 136


                  ..
gi 2057765590 981 DF 982
Cdd:cd18727   137 EG 138
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 327-640 1.42e-21

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: 95.94  E-value: 1.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 327 ASRWYRLGIHLNSNNGKFYHHLAILASQ--DELKALYYYCRSLMVNTPFMSTRESLVALFglDNMRQKPKGNRGYLQRDN 404
Cdd:pfam10373   1 ALRYYLLAILLLPSNGEPYNQLGVIALYvgNHLDAVYYFLRSLLSRNPFPTAKNNLELLF--DKIRSKLEQGELKLSPES 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 405 SKLKNYLDNQP-VENLFVRLHGMLFTKIGLEHFDETFQSFLDKlLKTNTFQRTSNSNRHWMEFYLFLAVINLSGLYNygn 483
Cdd:pfam10373  79 LQEGTPGDLLErLISLFLYLHGKLYTPTDFSEFPELEDEVLKK-LEILLKESLLSRYLKSRSLLLKMLLINIFAFEN--- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 484 enfiigkaqaakNKDDIQSLDADPIFAQES-RLTFIIMNHFMLKYLESEAYQPGHEVSEGWLLYCEIIMLWMVasgifdg 562
Cdd:pfam10373 155 ------------AKDKSSPEETKQFLLRLAlRFFFTLFGLLLEEVNTLEALKSFTPVATRYLPALRVYLCWLK------- 215

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2057765590 563 fangSNNSTWEKIMRKSDFpgsWEVFARFLTNithqIPSTTKEKILDSVNNDIEQESivqiqppALAEDWELRGISLL 640
Cdd:pfam10373 216 ----SNPSVLEFEDKDEKL---VDSLSDLWNE----LLSSTLLNSSFDVEKRPKRDY-------LLEEDVELKGFSPL 275
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 829-980 3.53e-21

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: 90.37  E-value: 3.53e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 829 IIVDTNCLIGDLEIVKKViqSEKWVVIVPSIVVTELDGLKYNPPP----LGHAAHEALEYLNETL--STKKIRIQTSKGN 902
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNF--GEENDVVIPITVLEELDGLKKGSDEsgreLARLARQANRWLDELLenNGGRLRGQTLDER 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2057765590 903 YltdisfseefdfgNGEDKKKNlDDLILGICLWHSKHNEknglhdksnenNEVTVLLTNDRNLRVKARARGVNVVGVK 980
Cdd:pfam13638  79 L-------------PPDPFDKN-DNRILAVALYLKEELP-----------DRPVILVSKDINLRIKADALGIPAEDYE 131
PIN_VapC_PhoHL-ATPase cd09883
VapC-like PIN domain of bacterial Smg6-like proteins with C-terminal PhoH-like ATPase domains; ...
 830-976 1.71e-15

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: 74.50  E-value: 1.71e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 830 IVDTNCLIGDLEIVKKViqsEKWVVIVPSIVVTELDGLKYNPPPLGHAAHEALEYLNETLSTKKIR--IQTSKGNYLTDI 907
Cdd:cd09883     5 VLDTNVLLHDPNAIFKF---EDNDVVIPITVLEELDKLKKRNDELGRNAREAIRNLDELREKGSLAegVPLENGGTLRVE 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2057765590 908 SFSEEFDFGNGEDKKKNlDDLILGICLWHSKhneknglhdksnENNEVTVLLTNDRNLRVKARARGVNV 976
Cdd:cd09883    82 LNHKDLLPLPELDLDKN-DNRILAVALKLKE------------EGDRPVILVTKDINLRIKADALGIKA 137
YlaK COG1875
Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General ...
 830-976 3.30e-08

Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General function prediction only];


Pssm-ID: 441479 [Multi-domain]  Cd Length: 441  Bit Score: 57.02  E-value: 3.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 830 IVDTNCLIGDLEIVKKViqsEKWVVIVPSIVVTELDGLKYNPPPLGHAAHEALEYLNETLSTKKIR--IQTSKGNYLTDI 907
Cdd:COG1875     8 VLDTNVLLHDPNAIFRF---EEHDVVIPMVVLEELDKFKKGMSELGRNARQASRLLDELRAKGNLDegVPLPNGGTLRVE 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2057765590 908 SFSEEFDFGNGEDKKKNlDDLILGICLwhskhneknGLHDKSNENNevTVLLTNDRNLRVKARARGVNV 976
Cdd:COG1875    85 LNHKDSELPAGLPLDKN-DNRILAVAL---------NLQEEYPGRP--VILVSKDINLRIKADALGLEA 141
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 215-308 2.54e-07

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: 49.62  E-value: 2.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 215 DIESKCWKLGFYSLIEQFRSAVN-LDRRRSKNRITSSF-VISNQFSIFLDEAEIFYKRLLKHVAdgTKSIDKSIEKNKpp 292
Cdd:pfam10374   1 KVLDLLWRKTHYPIIKWFRKWRKrLDGNSKKKKYPVEFrKLNSKLRKFLKSAQKFYYGLIQRLV--SREASSSLTALA-- 76

                          90
                  ....*....|....*...
gi 2057765590 293 KWI--RCVCCLGDVTRYR 308
Cdd:pfam10374  77 LLSchRCLIYLGDLHRYR 94
PIN_Smg5-like cd09884
VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar ...
 829-982 6.78e-06

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: 47.27  E-value: 6.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 829 IIVDTNCLIGDLEIVKKVIQSEKWVVIVPSIVVTELDGLKYNPPplghAAHEALEYL----------------NETLSTK 892
Cdd:cd09884     3 LVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKKESA----GAREAIRWLeaefkkgnryiraqkpNEKLPLP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590 893 KIRIQTSKGnylTDIS-FSEEFDF--------GNGEDKKKNLDDLILGIClwhskhnekngLHDKSNENNEVTVLltndr 963
Cdd:cd09884    79 LLKRPKKKD---RDAWrLYQILDCckylaqqqGDGEEDGAGMVTLLTGND-----------LDEKEAFNKGFSVL----- 139

                         170
                  ....*....|....*....
gi 2057765590 964 nlrVKARARGVNVVGVKDF 982
Cdd:cd09884   140 ---GAAHAAGVEIENILDF 155
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 829-967 2.10e-03

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: 38.94  E-value: 2.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057765590  829 IIVDTNCLIGDL--EIVKKVIQSEKwVVIVPSIVVTELDGLKYnppplghaahEALEYLNETLSTKKIRIQTSKGNyltd 906
Cdd:smart00670   3 VVLDTNVLIDGLirDALEKLLEKKG-EVYIPQTVLEELEYLAL----------RSLKKLEELALEGKIILKVLKEE---- 67

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2057765590  907 isFSEEFDFGNGEDKKKNL--DDLILGICLWHSKHneknglhdksnennevtVLLTNDRNLRV 967
Cdd:smart00670  68 --RIEEEILERLSLKLELLpnDALILATAKELGNV-----------------VLVTNDRDLRR 111
 
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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