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Conserved domains on  [gi|157818335|ref|NP_001101999|]
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endoribonuclease YbeY [Rattus norvegicus]

Protein Classification

rRNA maturation RNAse YbeY( domain architecture ID 10015425)

rRNA maturation RNAse YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of 16S rRNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 35-148 8.46e-38

rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member sequence only in nearly every bacterium. Crystallography demonstrated metal-binding activity, possibly to nickel. It is a predicted to be a metallohydrolase, and more recently it was shown that mutants have a ribosomal RNA processing defect. [Protein synthesis, Other]


:

Pssm-ID: 272871 [Multi-domain]  Cd Length: 110  Bit Score: 125.07  E-value: 8.46e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818335   35 FDLGIICVDNKNIQNINRIYRNKNVPTDVLSFPFHENLKAGEFPqprspdDYNLGDVFLGVEYIFQYCKG-NEDYYDVLT 113
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGGFP------EEVLGDIVISLEVAKEQAKEyGHSLERELA 74

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 157818335  114 VTATHGLCHLLGFTHSSEAEWQKMYNQEKLVLEEL 148
Cdd:TIGR00043  75 HLTVHGLLHLLGYDHETEDEEKEMFALEEEILALL 109
 
Name Accession Description Interval E-value
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 35-148 8.46e-38

rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member sequence only in nearly every bacterium. Crystallography demonstrated metal-binding activity, possibly to nickel. It is a predicted to be a metallohydrolase, and more recently it was shown that mutants have a ribosomal RNA processing defect. [Protein synthesis, Other]


Pssm-ID: 272871 [Multi-domain]  Cd Length: 110  Bit Score: 125.07  E-value: 8.46e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818335   35 FDLGIICVDNKNIQNINRIYRNKNVPTDVLSFPFHENLKAGEFPqprspdDYNLGDVFLGVEYIFQYCKG-NEDYYDVLT 113
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGGFP------EEVLGDIVISLEVAKEQAKEyGHSLERELA 74

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 157818335  114 VTATHGLCHLLGFTHSSEAEWQKMYNQEKLVLEEL 148
Cdd:TIGR00043  75 HLTVHGLLHLLGYDHETEDEEKEMFALEEEILALL 109
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 1-148 4.61e-27

ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and biogenesis]; ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440088  Cd Length: 144  Bit Score: 98.69  E-value: 4.61e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818335   1 MSLVIKNLQRVvPIRRMPLRRKMDLVRSILGVKK-FDLGIICVDNKNIQNINRIYRNKNVPTDVLSFPFHENLKAGEFPq 79
Cdd:COG0319    1 MSIEIQNEDDF-ELDEALLERWLEAALEAEGLAEdAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPL- 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157818335  80 prspddynLGDVFLGVEYIF----QYCKGNEDYYDVLTVtatHGLCHLLGFTHSSEAEWQKMYNQEKLVLEEL 148
Cdd:COG0319   79 --------LGDIVISVETAAreakEQGHSFEDELAHLLV---HGLLHLLGYDHETEEEAEEMEALEEEILAKL 140
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 24-148 6.95e-26

Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not properly maturated 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. It is involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs. The crystal structure of the protein from Aquifex aeolicus showed an overall fold consisting of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices.


Pssm-ID: 460455  Cd Length: 125  Bit Score: 95.23  E-value: 6.95e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818335   24 DLVRSILGVKKFD----LGIICVDNKNIQNINRIYRNKNVPTDVLSFPFHEnlkagefpqprspDDYNLGDVFLGVEYIF 99
Cdd:pfam02130   9 LVLEAALDEEKVPyeaeVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDE-------------PEEPLGDIVISPEKAK 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 157818335  100 ----QYCKGNEDYYDVLTVtatHGLCHLLGFTHSSEAEWQKMYNQEKLVLEEL 148
Cdd:pfam02130  76 eqaeEYGHSLERELAFLTV---HGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
PLN02887 PLN02887
hydrolase family protein
 31-148 1.36e-07

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 49.87  E-value: 1.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818335  31 GVKKFDLGIICVDNKNIQNINRIYRNKNVPTDVLSFPFHenlkageFPQPRSPDdYNLGDVFLGVEYIF-QYCKGNEDYY 109
Cdd:PLN02887 156 GYDSVELSVMLCNDDFIRKLNKEWRGEDHATDVLSMSQH-------VPGLKLPV-LMLGDIVISVETAArQAEERGHTLL 227

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 157818335 110 DVLTVTATHGLCHLLGFTH--SSEAEwQKMYNQEKLVLEEL 148
Cdd:PLN02887 228 DEIRILVVHGLLHLLGFDHeiSNEAE-AEMEKEEELLLKSL 267
 
Name Accession Description Interval E-value
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 35-148 8.46e-38

rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member sequence only in nearly every bacterium. Crystallography demonstrated metal-binding activity, possibly to nickel. It is a predicted to be a metallohydrolase, and more recently it was shown that mutants have a ribosomal RNA processing defect. [Protein synthesis, Other]


Pssm-ID: 272871 [Multi-domain]  Cd Length: 110  Bit Score: 125.07  E-value: 8.46e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818335   35 FDLGIICVDNKNIQNINRIYRNKNVPTDVLSFPFHENLKAGEFPqprspdDYNLGDVFLGVEYIFQYCKG-NEDYYDVLT 113
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGGFP------EEVLGDIVISLEVAKEQAKEyGHSLERELA 74

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 157818335  114 VTATHGLCHLLGFTHSSEAEWQKMYNQEKLVLEEL 148
Cdd:TIGR00043  75 HLTVHGLLHLLGYDHETEDEEKEMFALEEEILALL 109
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 1-148 4.61e-27

ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and biogenesis]; ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440088  Cd Length: 144  Bit Score: 98.69  E-value: 4.61e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818335   1 MSLVIKNLQRVvPIRRMPLRRKMDLVRSILGVKK-FDLGIICVDNKNIQNINRIYRNKNVPTDVLSFPFHENLKAGEFPq 79
Cdd:COG0319    1 MSIEIQNEDDF-ELDEALLERWLEAALEAEGLAEdAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPL- 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157818335  80 prspddynLGDVFLGVEYIF----QYCKGNEDYYDVLTVtatHGLCHLLGFTHSSEAEWQKMYNQEKLVLEEL 148
Cdd:COG0319   79 --------LGDIVISVETAAreakEQGHSFEDELAHLLV---HGLLHLLGYDHETEEEAEEMEALEEEILAKL 140
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 24-148 6.95e-26

Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not properly maturated 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. It is involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs. The crystal structure of the protein from Aquifex aeolicus showed an overall fold consisting of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices.


Pssm-ID: 460455  Cd Length: 125  Bit Score: 95.23  E-value: 6.95e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818335   24 DLVRSILGVKKFD----LGIICVDNKNIQNINRIYRNKNVPTDVLSFPFHEnlkagefpqprspDDYNLGDVFLGVEYIF 99
Cdd:pfam02130   9 LVLEAALDEEKVPyeaeVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDE-------------PEEPLGDIVISPEKAK 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 157818335  100 ----QYCKGNEDYYDVLTVtatHGLCHLLGFTHSSEAEWQKMYNQEKLVLEEL 148
Cdd:pfam02130  76 eqaeEYGHSLERELAFLTV---HGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
PLN02887 PLN02887
hydrolase family protein
 31-148 1.36e-07

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 49.87  E-value: 1.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818335  31 GVKKFDLGIICVDNKNIQNINRIYRNKNVPTDVLSFPFHenlkageFPQPRSPDdYNLGDVFLGVEYIF-QYCKGNEDYY 109
Cdd:PLN02887 156 GYDSVELSVMLCNDDFIRKLNKEWRGEDHATDVLSMSQH-------VPGLKLPV-LMLGDIVISVETAArQAEERGHTLL 227

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 157818335 110 DVLTVTATHGLCHLLGFTH--SSEAEwQKMYNQEKLVLEEL 148
Cdd:PLN02887 228 DEIRILVVHGLLHLLGFDHeiSNEAE-AEMEKEEELLLKSL 267
 
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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