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Conserved domains on  [gi|398365997|ref|NP_013467|]
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Nmd4p [Saccharomyces cerevisiae S288C]

Protein Classification

nonsense-mediated decay protein 4( domain architecture ID 13036795)

nonsense-mediated decay protein 4 is involved in nonsense-mediated decay of mRNAs containing premature stop codons

Gene Ontology:  GO:0000184

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_ScNmd4p-like cd18717
VapC-like PIN domain of Saccharomyces cerevisiae Nmd4p and related proteins; Saccharomyces ...
 7-155 5.03e-88

VapC-like PIN domain of Saccharomyces cerevisiae Nmd4p and related proteins; Saccharomyces cerevisiae Nmd4p may be involved in nonsense-mediated mRNA decay. This subfamily 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. 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: 350284  Cd Length: 150  Bit Score: 256.17  E-value: 5.03e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365997   7 IIDASAFEKGLGNIKRWCSDCT--EAVTLNFYIPTFTLNELDFLQQRRKSFAARESLKFIDRLDDSkfANLKVFIEFPEV 84
Cdd:cd18717    1 ILDASAFEKGLGNIKRWCDDNTkqNKVTLNLYIPTYTLQELDFLQYKRKSFNAKEALKFIDELTNS--QNFKLIIEFPEI 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 398365997  85 LDIILWSDVME-HNDSSGKINIAKLPKRLKNLLKSCIYKCYLEGNEGLHWFLISEDPQIREMAMQCNIPSCS 155
Cdd:cd18717   79 LDAILWSDVLRfSEGSLGKDSINKLPRRFKNLLKSCVYKCHLEENDDKKWILVTEDPKVREIADQCNIPWCS 150
 
Name Accession Description Interval E-value
PIN_ScNmd4p-like cd18717
VapC-like PIN domain of Saccharomyces cerevisiae Nmd4p and related proteins; Saccharomyces ...
 7-155 5.03e-88

VapC-like PIN domain of Saccharomyces cerevisiae Nmd4p and related proteins; Saccharomyces cerevisiae Nmd4p may be involved in nonsense-mediated mRNA decay. This subfamily 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. 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: 350284  Cd Length: 150  Bit Score: 256.17  E-value: 5.03e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365997   7 IIDASAFEKGLGNIKRWCSDCT--EAVTLNFYIPTFTLNELDFLQQRRKSFAARESLKFIDRLDDSkfANLKVFIEFPEV 84
Cdd:cd18717    1 ILDASAFEKGLGNIKRWCDDNTkqNKVTLNLYIPTYTLQELDFLQYKRKSFNAKEALKFIDELTNS--QNFKLIIEFPEI 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 398365997  85 LDIILWSDVME-HNDSSGKINIAKLPKRLKNLLKSCIYKCYLEGNEGLHWFLISEDPQIREMAMQCNIPSCS 155
Cdd:cd18717   79 LDAILWSDVLRfSEGSLGKDSINKLPRRFKNLLKSCVYKCHLEENDDKKWILVTEDPKVREIADQCNIPWCS 150
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 4-144 3.13e-04

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: 3.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365997     4 YNFIIDASAFekgLGNIKRWCSDCTEAVTLNFYIPTFTLNELDFLqqrrksfaARESLKFIDRLDDSKFANLKVFIEFPe 83
Cdd:smart00670   1 MKVVLDTNVL---IDGLIRDALEKLLEKKGEVYIPQTVLEELEYL--------ALRSLKKLEELALEGKIILKVLKEER- 68

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 398365997    84 vldiiLWSDVMEHNDSSgkiniAKLPKRLKNLLKSCIYKCylegneglHWFLISEDPQIRE 144
Cdd:smart00670  69 -----IEEEILERLSLK-----LELLPNDALILATAKELG--------NVVLVTNDRDLRR 111
 
Name Accession Description Interval E-value
PIN_ScNmd4p-like cd18717
VapC-like PIN domain of Saccharomyces cerevisiae Nmd4p and related proteins; Saccharomyces ...
 7-155 5.03e-88

VapC-like PIN domain of Saccharomyces cerevisiae Nmd4p and related proteins; Saccharomyces cerevisiae Nmd4p may be involved in nonsense-mediated mRNA decay. This subfamily 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. 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: 350284  Cd Length: 150  Bit Score: 256.17  E-value: 5.03e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365997   7 IIDASAFEKGLGNIKRWCSDCT--EAVTLNFYIPTFTLNELDFLQQRRKSFAARESLKFIDRLDDSkfANLKVFIEFPEV 84
Cdd:cd18717    1 ILDASAFEKGLGNIKRWCDDNTkqNKVTLNLYIPTYTLQELDFLQYKRKSFNAKEALKFIDELTNS--QNFKLIIEFPEI 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 398365997  85 LDIILWSDVME-HNDSSGKINIAKLPKRLKNLLKSCIYKCYLEGNEGLHWFLISEDPQIREMAMQCNIPSCS 155
Cdd:cd18717   79 LDAILWSDVLRfSEGSLGKDSINKLPRRFKNLLKSCVYKCHLEENDDKKWILVTEDPKVREIADQCNIPWCS 150
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 7-147 3.07e-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: 39.57  E-value: 3.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365997   7 IIDASAFEKGLG-----NIKRWCSDCTEAvTLNFYIPTFTLNELDFLQQRRksFAARESLKFIDRLDDskfanLKVFIEF 81
Cdd:cd09854    1 VLDTNVLIALLSsepesEAAKELLALLLG-DSELVIPPLVLAELLRLLARE--RGARRALEILELLRA-----LEVVEEE 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 398365997  82 PEVLDIILWsdvmehndsSGKINIAKLPKRLKNLLKSCIYKCylegnegLHWFLISEDPQIREMAM 147
Cdd:cd09854   73 PALAEIALE---------VLALGLERGLDFGDALILALAKEL-------GGAVLVTNDRDFRRLAK 122
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 4-144 3.13e-04

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: 3.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365997     4 YNFIIDASAFekgLGNIKRWCSDCTEAVTLNFYIPTFTLNELDFLqqrrksfaARESLKFIDRLDDSKFANLKVFIEFPe 83
Cdd:smart00670   1 MKVVLDTNVL---IDGLIRDALEKLLEKKGEVYIPQTVLEELEYL--------ALRSLKKLEELALEGKIILKVLKEER- 68

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 398365997    84 vldiiLWSDVMEHNDSSgkiniAKLPKRLKNLLKSCIYKCylegneglHWFLISEDPQIRE 144
Cdd:smart00670  69 -----IEEEILERLSLK-----LELLPNDALILATAKELG--------NVVLVTNDRDLRR 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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