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Conserved domains on  [gi|378744173|ref|NP_001243756|]
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telomerase-binding protein EST1A isoform 3 [Homo sapiens]

Protein Classification

EST1_DNA_bind and PIN_Smg6 domain-containing protein( domain architecture ID 11860023)

EST1_DNA_bind and PIN_Smg6 domain-containing protein

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 ...
 333-508 5.18e-100

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: 298.40  E-value: 5.18e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 333 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLEQRFE 411
Cdd:cd09885    1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 412 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVK 490
Cdd:cd09885   81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                        170
                 ....*....|....*...
gi 378744173 491 ALTRNVPVRDIPAFLTWA 508
Cdd:cd09885  161 ALSRNIPVRDLPSFLKWA 178
EST1_DNA_bind super family cl26538
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 1-195 9.05e-15

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: 74.76  E-value: 9.05e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173    1 METFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKdcfSEECRSVIQEQAAALGLAmFSLLVRR 77
Cdd:pfam10373 108 FSEFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDK---SSPEETKQFLLRLALRFF-FTLFGLL 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173   78 CTCLLKESAKAQLSspedqddqddikvssfvPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPSHVAVDVWSTLADFC 157
Cdd:pfam10373 184 LEEVNTLEALKSFT-----------------PVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLW 238

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 378744173  158 NILTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 195
Cdd:pfam10373 239 NELLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
 
Name Accession Description Interval E-value
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 333-508 5.18e-100

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: 298.40  E-value: 5.18e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 333 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLEQRFE 411
Cdd:cd09885    1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 412 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVK 490
Cdd:cd09885   81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                        170
                 ....*....|....*...
gi 378744173 491 ALTRNVPVRDIPAFLTWA 508
Cdd:cd09885  161 ALSRNIPVRDLPSFLKWA 178
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 340-500 1.82e-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: 95.76  E-value: 1.82e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173  340 LVPDTNGFIDHLASLARLLEsrKYILVVPLIVINELDGLAKGQETDHRaggyarVVQEKARKSIEFLEQRFESRDSCLRA 419
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNFGE--ENDVVIPITVLEELDGLKKGSDESGR------ELARLARQANRWLDELLENNGGRLRG 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173  420 LTSRGNELESIAFRseditgqlgnNDDLILSCCLHYckdkakdfmpaSKEEPIRllrEVVLLTDDRNLRVKALTRNVPVR 499
Cdd:pfam13638  73 QTLDERLPPDPFDK----------NDNRILAVALYL-----------KEELPDR---PVILVSKDINLRIKADALGIPAE 128


                  .
gi 378744173  500 D 500
Cdd:pfam13638 129 D 129
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 1-195 9.05e-15

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: 74.76  E-value: 9.05e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173    1 METFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKdcfSEECRSVIQEQAAALGLAmFSLLVRR 77
Cdd:pfam10373 108 FSEFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDK---SSPEETKQFLLRLALRFF-FTLFGLL 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173   78 CTCLLKESAKAQLSspedqddqddikvssfvPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPSHVAVDVWSTLADFC 157
Cdd:pfam10373 184 LEEVNTLEALKSFT-----------------PVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLW 238

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 378744173  158 NILTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 195
Cdd:pfam10373 239 NELLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 340-489 2.88e-11

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: 60.52  E-value: 2.88e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173   340 LVPDTNGFIDHLAS-LARLLESRKYILVVPLIVINELDGLAKgqetdHRAGGYARVVQEKARKSIEFLEQRFESRdsclr 418
Cdd:smart00670   3 VVLDTNVLIDGLIRdALEKLLEKKGEVYIPQTVLEELEYLAL-----RSLKKLEELALEGKIILKVLKEERIEEE----- 72

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 378744173   419 altsrgnELESIAFRSEDITgqlgnNDDLILSCCLHYCKdkakdfmpaskeepirllreVVLLTDDRNLRV 489
Cdd:smart00670  73 -------ILERLSLKLELLP-----NDALILATAKELGN--------------------VVLVTNDRDLRR 111
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
341-498 1.28e-05

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


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 44.43  E-value: 1.28e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 341 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQetdhrAGGYARvvqeKARKSIEFLEQrfesr 413
Cdd:COG1412    4 LLDTNALmmpaqfgVDVFEELDRLL--GKYEFIVPEAVLEELEKLSRGA-----KGKEKR----AARVALDLAER----- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 414 dsclraltsrgnelesiaFRSEDITGqlGNNDDLILSCCLHYckdkakdfmpaskeepirllrEVVLLTDDRNLRVKALT 493
Cdd:COG1412   68 ------------------CEIVETEG--GYADDAILELAKEN---------------------GVIVATNDKELRRRLLE 106


                 ....*
gi 378744173 494 RNVPV 498
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 ...
 333-508 5.18e-100

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: 298.40  E-value: 5.18e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 333 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLEQRFE 411
Cdd:cd09885    1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 412 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVK 490
Cdd:cd09885   81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                        170
                 ....*....|....*...
gi 378744173 491 ALTRNVPVRDIPAFLTWA 508
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 ...
 341-507 5.90e-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: 165.54  E-value: 5.90e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 341 VPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETdhraggyarvVQEKARKSIEFLEQRFESRDSCLRAL 420
Cdd:cd09880    1 VFDTNILLSHLDVLKLLVESGKWTVVIPLIVITELDGLKKNPDP----------LGPKARSALRYIEACLKKHSRWLRVQ 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 421 TSRGNELESIAFRSE----DITGQLGNNDDLILSCCLHYCKDKAKDFMPASKeepirllreVVLLTDDRNLRVKALTRNV 496
Cdd:cd09880   71 TSKGNYLADLTIRSEqlsdASELRRRNNDDRILECALWQQKHFVDREDGDGK---------VVLVTNDRNLRLKARARGV 141

                        170
                 ....*....|.
gi 378744173 497 PVRDIPAFLTW 507
Cdd:cd09880  142 EAVTVKELLKS 152
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 341-507 1.63e-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: 104.56  E-value: 1.63e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 341 VPDTNGFIDHLASLARLLE-----SRKYILVVPLIVINELDGLAKGQETDHraggyarvVQEKARKSIEFLEQRFESRDS 415
Cdd:cd18727    1 VLDTNVLISHLDLLKQLVEdveklSLPVVIVIPWVVLQELDGLKKSKRKSS--------LGWLARRASTWLLEKLRSKHP 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 416 CLRALTsrgnelesiafRSEDITGQ---LGNNDDLILSCCLHYCKdkakdfmpaskeepiRLLREVVLLTDDRNLRVKAL 492
Cdd:cd18727   73 RVRGQA-----------LSETLRASgdpGESNDDAILDCCLYFQE---------------KYGAPVVLLSNDKNLCNKAL 126

                        170
                 ....*....|....*
gi 378744173 493 TRNVPVRDIPAFLTW 507
Cdd:cd18727  127 INGIPTISPEEGMTA 141
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 340-500 1.82e-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: 95.76  E-value: 1.82e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173  340 LVPDTNGFIDHLASLARLLEsrKYILVVPLIVINELDGLAKGQETDHRaggyarVVQEKARKSIEFLEQRFESRDSCLRA 419
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNFGE--ENDVVIPITVLEELDGLKKGSDESGR------ELARLARQANRWLDELLENNGGRLRG 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173  420 LTSRGNELESIAFRseditgqlgnNDDLILSCCLHYckdkakdfmpaSKEEPIRllrEVVLLTDDRNLRVKALTRNVPVR 499
Cdd:pfam13638  73 QTLDERLPPDPFDK----------NDNRILAVALYL-----------KEELPDR---PVILVSKDINLRIKADALGIPAE 128


                  .
gi 378744173  500 D 500
Cdd:pfam13638 129 D 129
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 1-195 9.05e-15

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: 74.76  E-value: 9.05e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173    1 METFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKdcfSEECRSVIQEQAAALGLAmFSLLVRR 77
Cdd:pfam10373 108 FSEFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDK---SSPEETKQFLLRLALRFF-FTLFGLL 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173   78 CTCLLKESAKAQLSspedqddqddikvssfvPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPSHVAVDVWSTLADFC 157
Cdd:pfam10373 184 LEEVNTLEALKSFT-----------------PVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLW 238

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 378744173  158 NILTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 195
Cdd:pfam10373 239 NELLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
PIN_VapC_PhoHL-ATPase cd09883
VapC-like PIN domain of bacterial Smg6-like proteins with C-terminal PhoH-like ATPase domains; ...
 341-500 1.89e-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: 64.87  E-value: 1.89e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 341 VPDTNGFI-DHLAslarLLESRKYILVVPLIVINELDGLAKGQETDHRaggyarvvqeKARKSIEFLEQRFESRDSCLRA 419
Cdd:cd09883    5 VLDTNVLLhDPNA----IFKFEDNDVVIPITVLEELDKLKKRNDELGR----------NAREAIRNLDELREKGSLAEGV 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 420 LTSRGNELE-SIAFRSEDITGQL--GNNDDLILSCCLHYCKDKAKDfmpaskeepirllreVVLLTDDRNLRVKALTRNV 496
Cdd:cd09883   71 PLENGGTLRvELNHKDLLPLPELdlDKNDNRILAVALKLKEEGDRP---------------VILVTKDINLRIKADALGI 135


                 ....
gi 378744173 497 PVRD 500
Cdd:cd09883  136 KAED 139
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 340-489 2.88e-11

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: 60.52  E-value: 2.88e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173   340 LVPDTNGFIDHLAS-LARLLESRKYILVVPLIVINELDGLAKgqetdHRAGGYARVVQEKARKSIEFLEQRFESRdsclr 418
Cdd:smart00670   3 VVLDTNVLIDGLIRdALEKLLEKKGEVYIPQTVLEELEYLAL-----RSLKKLEELALEGKIILKVLKEERIEEE----- 72

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 378744173   419 altsrgnELESIAFRSEDITgqlgnNDDLILSCCLHYCKdkakdfmpaskeepirllreVVLLTDDRNLRV 489
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 ...
 339-426 4.37e-11

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: 61.14  E-value: 4.37e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 339 FLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKgqetdhraggyarvVQEKARKSIEFLEQRFESRDSCLR 418
Cdd:cd09884    2 YLVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKK--------------ESAGAREAIRWLEAEFKKGNRYIR 67


                 ....*...
gi 378744173 419 ALtsRGNE 426
Cdd:cd09884   68 AQ--KPNE 73
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
341-498 1.28e-05

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


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 44.43  E-value: 1.28e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 341 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQetdhrAGGYARvvqeKARKSIEFLEQrfesr 413
Cdd:COG1412    4 LLDTNALmmpaqfgVDVFEELDRLL--GKYEFIVPEAVLEELEKLSRGA-----KGKEKR----AARVALDLAER----- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 414 dsclraltsrgnelesiaFRSEDITGqlGNNDDLILSCCLHYckdkakdfmpaskeepirllrEVVLLTDDRNLRVKALT 493
Cdd:COG1412   68 ------------------CEIVETEG--GYADDAILELAKEN---------------------GVIVATNDKELRRRLLE 106


                 ....*
gi 378744173 494 RNVPV 498
Cdd:COG1412  107 AGIPV 111
YlaK COG1875
Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General ...
 365-491 2.27e-05

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: 46.62  E-value: 2.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 365 LVVPLIVINELDGLAKGQ-ETdhragGYArvvqekARKSIEFLEQrfesrdsclraLTSRGN-----ELES---IAFRSE 435
Cdd:COG1875   29 VVIPMVVLEELDKFKKGMsEL-----GRN------ARQASRLLDE-----------LRAKGNldegvPLPNggtLRVELN 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 378744173 436 DITGQL------GNNDDLILSCCLHYCKDKAKdfmpaskeepirllREVVLLTDDRNLRVKA 491
Cdd:COG1875   87 HKDSELpaglplDKNDNRILAVALNLQEEYPG--------------RPVILVSKDINLRIKA 134
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 341-499 1.56e-04

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: 41.49  E-value: 1.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 341 VPDTNGFIDHLAS------LARLLESR--KYILVVPLIVINELDGLAKGQETDHRAggyarvvqEKARKSIEFLEQRFES 412
Cdd:cd09854    1 VLDTNVLIALLSSepeseaAKELLALLlgDSELVIPPLVLAELLRLLARERGARRA--------LEILELLRALEVVEEE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 413 RDSclraltsrgnELESIAFRSEDITGQLGNNDDLILSCCLHYckdkakdfmpaskeepirllREVVLLTDDRNLRvKAL 492
Cdd:cd09854   73 PAL----------AEIALEVLALGLERGLDFGDALILALAKEL--------------------GGAVLVTNDRDFR-RLA 121


                 ....*..
gi 378744173 493 TRNVPVR 499
Cdd:cd09854  122 KLGLKVI 128
PIN_VapC_AF0591-like cd09879
VapC-like PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal ...
 341-498 7.06e-04

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: 39.37  E-value: 7.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 341 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQETDHRAggYARVvqekARKSIEfleqRFESR 413
Cdd:cd09879    2 ILDTNFLmypfqfgVDIFEELERLL--GKYEIVVPSAVIEELERLAKKGKGKDKR--AARL----ALKLAE----RCKVV 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378744173 414 DsclraltsrgnelesiafrSEDITGqlgnnDDLIlsccLHYCKDKakdfmpaskeepirllrEVVLLTDDRNLRVKALT 493
Cdd:cd09879   70 E-------------------SEGEPA-----DDAI----LELAKEL-----------------GAIVATNDRELRKRLRE 104


                 ....*
gi 378744173 494 RNVPV 498
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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