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Conserved domains on  [gi|47117865|sp|P58557|]
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RecName: Full=Endoribonuclease YbeY

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 ...
 35-149 1.49e-46

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: 147.41  E-value: 1.49e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47117865    35 FDLGIICVDNKNIQHINRIYRDRNVPTDVLSFPFHEHLKAGEFPqpdfpdDYNLGDIFLGVEYIFHQCKE-NEDYNDVLT 113
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGGFP------EEVLGDIVISLEVAKEQAKEyGHSLERELA 74

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 47117865   114 VTATHGLCHLLGFTHGTEAEWQQMFQKEKAVLDELG 149
Cdd:TIGR00043  75 HLTVHGLLHLLGYDHETEDEEKEMFALEEEILALLG 110
 
Name Accession Description Interval E-value
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 35-149 1.49e-46

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: 147.41  E-value: 1.49e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47117865    35 FDLGIICVDNKNIQHINRIYRDRNVPTDVLSFPFHEHLKAGEFPqpdfpdDYNLGDIFLGVEYIFHQCKE-NEDYNDVLT 113
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGGFP------EEVLGDIVISLEVAKEQAKEyGHSLERELA 74

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 47117865   114 VTATHGLCHLLGFTHGTEAEWQQMFQKEKAVLDELG 149
Cdd:TIGR00043  75 HLTVHGLLHLLGYDHETEDEEKEMFALEEEILALLG 110
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 1-149 1.71e-31

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: 110.25  E-value: 1.71e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47117865   1 MSLVIRNLQRViPIRRAPLRSKIEIVRRILGVQK-FDLGIICVDNKNIQHINRIYRDRNVPTDVLSFPFHEhlkagefpq 79
Cdd:COG0319   1 MSIEIQNEDDF-ELDEALLERWLEAALEAEGLAEdAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDE--------- 70

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 47117865  80 PDFPDDYNLGDIFLGVEYIFHQCKE-NEDYNDVLTVTATHGLCHLLGFTHGTEAEWQQMFQKEKAVLDELG 149
Cdd:COG0319  71 LPEDGPPLLGDIVISVETAAREAKEqGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLG 141
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 24-148 1.59e-29

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: 104.86  E-value: 1.59e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47117865    24 EIVRRILGVQKFD----LGIICVDNKNIQHINRIYRDRNVPTDVLSFPFHEhlkagefpqpdfpDDYNLGDIFLGVEYIF 99
Cdd:pfam02130   9 LVLEAALDEEKVPyeaeVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDE-------------PEEPLGDIVISPEKAK 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 47117865   100 HQCKE-NEDYNDVLTVTATHGLCHLLGFTHGTEAEWQQMFQKEKAVLDEL 148
Cdd:pfam02130  76 EQAEEyGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
PLN02887 PLN02887
hydrolase family protein
 31-145 3.84e-10

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 57.19  E-value: 3.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47117865   31 GVQKFDLGIICVDNKNIQHINRIYRDRNVPTDVLSFPFHehlkageFPQPDFPDdYNLGDIFLGVEYIFHQCKEN-EDYN 109
Cdd:PLN02887 156 GYDSVELSVMLCNDDFIRKLNKEWRGEDHATDVLSMSQH-------VPGLKLPV-LMLGDIVISVETAARQAEERgHTLL 227

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 47117865  110 DVLTVTATHGLCHLLGFTHGTEAEWQQMFQKEKAVL 145
Cdd:PLN02887 228 DEIRILVVHGLLHLLGFDHEISNEAEAEMEKEEELL 263
 
Name Accession Description Interval E-value
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 35-149 1.49e-46

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: 147.41  E-value: 1.49e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47117865    35 FDLGIICVDNKNIQHINRIYRDRNVPTDVLSFPFHEHLKAGEFPqpdfpdDYNLGDIFLGVEYIFHQCKE-NEDYNDVLT 113
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGGFP------EEVLGDIVISLEVAKEQAKEyGHSLERELA 74

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 47117865   114 VTATHGLCHLLGFTHGTEAEWQQMFQKEKAVLDELG 149
Cdd:TIGR00043  75 HLTVHGLLHLLGYDHETEDEEKEMFALEEEILALLG 110
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 1-149 1.71e-31

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: 110.25  E-value: 1.71e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47117865   1 MSLVIRNLQRViPIRRAPLRSKIEIVRRILGVQK-FDLGIICVDNKNIQHINRIYRDRNVPTDVLSFPFHEhlkagefpq 79
Cdd:COG0319   1 MSIEIQNEDDF-ELDEALLERWLEAALEAEGLAEdAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDE--------- 70

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 47117865  80 PDFPDDYNLGDIFLGVEYIFHQCKE-NEDYNDVLTVTATHGLCHLLGFTHGTEAEWQQMFQKEKAVLDELG 149
Cdd:COG0319  71 LPEDGPPLLGDIVISVETAAREAKEqGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLG 141
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 24-148 1.59e-29

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: 104.86  E-value: 1.59e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47117865    24 EIVRRILGVQKFD----LGIICVDNKNIQHINRIYRDRNVPTDVLSFPFHEhlkagefpqpdfpDDYNLGDIFLGVEYIF 99
Cdd:pfam02130   9 LVLEAALDEEKVPyeaeVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDE-------------PEEPLGDIVISPEKAK 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 47117865   100 HQCKE-NEDYNDVLTVTATHGLCHLLGFTHGTEAEWQQMFQKEKAVLDEL 148
Cdd:pfam02130  76 EQAEEyGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
PLN02887 PLN02887
hydrolase family protein
 31-145 3.84e-10

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 57.19  E-value: 3.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47117865   31 GVQKFDLGIICVDNKNIQHINRIYRDRNVPTDVLSFPFHehlkageFPQPDFPDdYNLGDIFLGVEYIFHQCKEN-EDYN 109
Cdd:PLN02887 156 GYDSVELSVMLCNDDFIRKLNKEWRGEDHATDVLSMSQH-------VPGLKLPV-LMLGDIVISVETAARQAEERgHTLL 227

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 47117865  110 DVLTVTATHGLCHLLGFTHGTEAEWQQMFQKEKAVL 145
Cdd:PLN02887 228 DEIRILVVHGLLHLLGFDHEISNEAEAEMEKEEELL 263
 
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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