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Conserved domains on  [gi|398365521|ref|NP_014809|]
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mRNA-processing endoribonuclease [Saccharomyces cerevisiae S288C]

Protein Classification

PIN_Swt1-like domain-containing protein( domain architecture ID 13036856)

PIN_Swt1-like domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 133-280 1.46e-52

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: 173.51  E-value: 1.46e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 133 VVDTNFIISHLNTLEKLRSL--SSTYHHLIIVPTTVIQELDGLKKSPDiardnddttnqehDRTIGTLARWGNDWIYKNL 210
Cdd:cd18727    1 VLDTNVLISHLDLLKQLVEDveKLSLPVVIVIPWVVLQELDGLKKSKR-------------KSSLGWLARRASTWLLEKL 67

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 398365521 211 ANLDSGLIGQKLKQSLN----PGSLKDDSILDCCLYFKEILNCFVILLSNDKNLCTKALTEDILTVSFRKNMDA 280
Cdd:cd18727   68 RSKHPRVRGQALSETLRasgdPGESNDDAILDCCLYFQEKYGAPVVLLSNDKNLCNKALINGIPTISPEEGMTA 141
 
Name Accession Description Interval E-value
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 133-280 1.46e-52

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: 173.51  E-value: 1.46e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 133 VVDTNFIISHLNTLEKLRSL--SSTYHHLIIVPTTVIQELDGLKKSPDiardnddttnqehDRTIGTLARWGNDWIYKNL 210
Cdd:cd18727    1 VLDTNVLISHLDLLKQLVEDveKLSLPVVIVIPWVVLQELDGLKKSKR-------------KSSLGWLARRASTWLLEKL 67

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 398365521 211 ANLDSGLIGQKLKQSLN----PGSLKDDSILDCCLYFKEILNCFVILLSNDKNLCTKALTEDILTVSFRKNMDA 280
Cdd:cd18727   68 RSKHPRVRGQALSETLRasgdPGESNDDAILDCCLYFQEKYGAPVVLLSNDKNLCNKALINGIPTISPEEGMTA 141
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 132-275 5.70e-39

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: 137.36  E-value: 5.70e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521  132 FVVDTNFIISHLNTLEKLRslsstYHHLIIVPTTVIQELDGLKKSPDiardnddttnqEHDRTIGTLARWGNDWIYKNLA 211
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNFG-----EENDVVIPITVLEELDGLKKGSD-----------ESGRELARLARQANRWLDELLE 64

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 398365521  212 NLDSGLIGQKLKQSLNPGSL--KDDSILDCCLYFK-EILNCFVILLSNDKNLCTKALTEDILTVSFR 275
Cdd:pfam13638  65 NNGGRLRGQTLDERLPPDPFdkNDNRILAVALYLKeELPDRPVILVSKDINLRIKADALGIPAEDYE 131
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 132-260 1.63e-09

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


Pssm-ID: 214771 [Multi-domain]  Cd Length: 111  Bit Score: 55.12  E-value: 1.63e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521   132 FVVDTNFIISHL--NTLEKLRSLsstyHHLIIVPTTVIQELDGLKkspdiardnddttnQEHDRTIGTLARWGNDWIYKN 209
Cdd:smart00670   3 VVLDTNVLIDGLirDALEKLLEK----KGEVYIPQTVLEELEYLA--------------LRSLKKLEELALEGKIILKVL 64

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 398365521   210 LANldsGLIGQKLKQSLNPGSLK--DDSILDCCLYFKEilncfVILLSNDKNL 260
Cdd:smart00670  65 KEE---RIEEEILERLSLKLELLpnDALILATAKELGN-----VVLVTNDRDL 109
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
133-276 8.50e-05

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


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 42.12  E-value: 8.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 133 VVDTNFII----SHLNTLEKLRSLSSTYHhlIIVPTTVIQELDGLKKspdiardnddttnqEHDRTIGTLARWGNDWIyK 208
Cdd:COG1412    4 LLDTNALMmpaqFGVDVFEELDRLLGKYE--FIVPEAVLEELEKLSR--------------GAKGKEKRAARVALDLA-E 66

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398365521 209 NLANLDSgligqklkqslnPGSLKDDSILDCCLYFKeilncfVILLSNDKNLCTKALTEDILTVSFRK 276
Cdd:COG1412   67 RCEIVET------------EGGYADDAILELAKENG------VIVATNDKELRRRLLEAGIPVIYLRQ 116
 
Name Accession Description Interval E-value
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 133-280 1.46e-52

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: 173.51  E-value: 1.46e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 133 VVDTNFIISHLNTLEKLRSL--SSTYHHLIIVPTTVIQELDGLKKSPDiardnddttnqehDRTIGTLARWGNDWIYKNL 210
Cdd:cd18727    1 VLDTNVLISHLDLLKQLVEDveKLSLPVVIVIPWVVLQELDGLKKSKR-------------KSSLGWLARRASTWLLEKL 67

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 398365521 211 ANLDSGLIGQKLKQSLN----PGSLKDDSILDCCLYFKEILNCFVILLSNDKNLCTKALTEDILTVSFRKNMDA 280
Cdd:cd18727   68 RSKHPRVRGQALSETLRasgdPGESNDDAILDCCLYFQEKYGAPVVLLSNDKNLCNKALINGIPTISPEEGMTA 141
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 132-275 5.70e-39

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: 137.36  E-value: 5.70e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521  132 FVVDTNFIISHLNTLEKLRslsstYHHLIIVPTTVIQELDGLKKSPDiardnddttnqEHDRTIGTLARWGNDWIYKNLA 211
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNFG-----EENDVVIPITVLEELDGLKKGSD-----------ESGRELARLARQANRWLDELLE 64

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 398365521  212 NLDSGLIGQKLKQSLNPGSL--KDDSILDCCLYFK-EILNCFVILLSNDKNLCTKALTEDILTVSFR 275
Cdd:pfam13638  65 NNGGRLRGQTLDERLPPDPFdkNDNRILAVALYLKeELPDRPVILVSKDINLRIKADALGIPAEDYE 131
PIN_Smg5-6-like cd09880
VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related ...
 133-273 2.38e-17

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: 78.87  E-value: 2.38e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 133 VVDTNFIISHLNTLEKLRSLSSTyhhLIIVPTTVIQELDGLKKSPDIARDNddttnqehdrtigtlARWGNDWIYKNLAN 212
Cdd:cd09880    1 VFDTNILLSHLDVLKLLVESGKW---TVVIPLIVITELDGLKKNPDPLGPK---------------ARSALRYIEACLKK 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 213 LDSGL------------IGQKLKQSLNPGSLK----DDSILDCCLYFKEIL------NCFVILLSNDKNLCTKALTEDIL 270
Cdd:cd09880   63 HSRWLrvqtskgnyladLTIRSEQLSDASELRrrnnDDRILECALWQQKHFvdredgDGKVVLVTNDRNLRLKARARGVE 142


                 ...
gi 398365521 271 TVS 273
Cdd:cd09880  143 AVT 145
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 133-269 5.82e-15

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: 72.68  E-value: 5.82e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 133 VVDTNFIISHLNTLEKLrslSSTYHHLIIVPTTVIQELDGLKKSpdiaRDNDDTTNQEHDRTIGTLARWGNDWIYKNLAN 212
Cdd:cd09885    9 VPDTNCFIDHLELIEKL---VESRKFTVLVPLIVVNELDGLAKG----SESDSYADEAHAEEVQAKARKAVKFLEEQFEA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 213 LDSGLIGQKLKQSL----------NPGSLK---DDSILDCCLYF---------------KEILNCFVILLSNDKNLCTKA 264
Cdd:cd09885   82 RNPYVRALTSKGTLldtiafrsedINDGDGgnnDDLILSCCLNLckdkavdfmpaskdqPIRLYREVVLLTDDRNLRVKA 161


                 ....*
gi 398365521 265 LTEDI 269
Cdd:cd09885  162 LSRNI 166
PIN_VapC_PhoHL-ATPase cd09883
VapC-like PIN domain of bacterial Smg6-like proteins with C-terminal PhoH-like ATPase domains; ...
 132-277 6.65e-11

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: 60.25  E-value: 6.65e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 132 FVVDTNFIISHLNTLEKLRSlsstyhHLIIVPTTVIQELDGLKKSPDI----ARdnddttnqEHDRTIGTLARWGndwiy 207
Cdd:cd09883    4 YVLDTNVLLHDPNAIFKFED------NDVVIPITVLEELDKLKKRNDElgrnAR--------EAIRNLDELREKG----- 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 208 kNLANLDSGLIGQKLKQSLNPGSLK----------DDSILDCCLYFKEILNCFVILLSNDKNLCTKALTEDILTVSFRKN 277
Cdd:cd09883   65 -SLAEGVPLENGGTLRVELNHKDLLplpeldldknDNRILAVALKLKEEGDRPVILVTKDINLRIKADALGIKAEDYETD 143
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 132-260 1.63e-09

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


Pssm-ID: 214771 [Multi-domain]  Cd Length: 111  Bit Score: 55.12  E-value: 1.63e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521   132 FVVDTNFIISHL--NTLEKLRSLsstyHHLIIVPTTVIQELDGLKkspdiardnddttnQEHDRTIGTLARWGNDWIYKN 209
Cdd:smart00670   3 VVLDTNVLIDGLirDALEKLLEK----KGEVYIPQTVLEELEYLA--------------LRSLKKLEELALEGKIILKVL 64

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 398365521   210 LANldsGLIGQKLKQSLNPGSLK--DDSILDCCLYFKEilncfVILLSNDKNL 260
Cdd:smart00670  65 KEE---RIEEEILERLSLKLELLpnDALILATAKELGN-----VVLVTNDRDL 109
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
133-276 8.50e-05

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


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 42.12  E-value: 8.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 133 VVDTNFII----SHLNTLEKLRSLSSTYHhlIIVPTTVIQELDGLKKspdiardnddttnqEHDRTIGTLARWGNDWIyK 208
Cdd:COG1412    4 LLDTNALMmpaqFGVDVFEELDRLLGKYE--FIVPEAVLEELEKLSR--------------GAKGKEKRAARVALDLA-E 66

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398365521 209 NLANLDSgligqklkqslnPGSLKDDSILDCCLYFKeilncfVILLSNDKNLCTKALTEDILTVSFRK 276
Cdd:COG1412   67 RCEIVET------------EGGYADDAILELAKENG------VIVATNDKELRRRLLEAGIPVIYLRQ 116
PIN_VapC_AF0591-like cd09879
VapC-like PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal ...
 133-276 1.08e-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: 41.68  E-value: 1.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 133 VVDTNFII----SHLNTLEKLRSLSSTYHhlIIVPTTVIQELDGLKKSpdiardnddttnqehdrtigtlaRWGNDWIYK 208
Cdd:cd09879    2 ILDTNFLMypfqFGVDIFEELERLLGKYE--IVVPSAVIEELERLAKK-----------------------GKGKDKRAA 56

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398365521 209 NLAnLDsgLIGQ-KLKQSlnPGSLKDDSILDCCLYfkeiLNCFVIllSNDKNLCTKALTEDILTVSFRK 276
Cdd:cd09879   57 RLA-LK--LAERcKVVES--EGEPADDAILELAKE----LGAIVA--TNDRELRKRLREKGIPVIYLRQ 114
YlaK COG1875
Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General ...
 132-264 3.98e-04

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: 42.77  E-value: 3.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 132 FVVDTNFIISHLNTLEKLRSlsstyhHLIIVPTTVIQELDGLKK-SPDIARDNDDTTnqehdRTIGTLarwgndwiyKNL 210
Cdd:COG1875    7 YVLDTNVLLHDPNAIFRFEE------HDVVIPMVVLEELDKFKKgMSELGRNARQAS-----RLLDEL---------RAK 66

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398365521 211 ANLDSGL--------------IGQKLKQSLnPGSLKDDSILDCCLYFK-EILNCFVILLSNDKNLCTKA 264
Cdd:COG1875   67 GNLDEGVplpnggtlrvelnhKDSELPAGL-PLDKNDNRILAVALNLQeEYPGRPVILVSKDINLRIKA 134
PIN_Smg5-like cd09884
VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar ...
 133-243 5.00e-04

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: 40.72  E-value: 5.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365521 133 VVDTNFIISHLNTLeklRSLSSTYHHLIIVPTTVIQELDGLKKSPDIARDnddttnqehdrTIgtlaRW-------GNDW 205
Cdd:cd09884    4 VPDTSALCDHLHLI---KQLVQSGKFIVIIPLAVIDGLDELKKESAGARE-----------AI----RWleaefkkGNRY 65

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 398365521 206 IyknLANLDsgliGQKLKQSLNPGSLKDDS-------ILDCCLYF 243
Cdd:cd09884   66 I---RAQKP----NEKLPLPLLKRPKKKDRdawrlyqILDCCKYL 103
 
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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