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Conserved domains on  [gi|226710479|sp|B1LLB0|]
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RecName: Full=Endoribonuclease YbeY

Protein Classification

rRNA maturation RNAse YbeY( domain architecture ID 10001064)

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

Gene Symbol:  ybeY
Gene Ontology:  GO:0006364|GO:0004222|GO:0004521

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 6-148 3.16e-55

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: 170.34  E-value: 3.16e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479   6 LDLQLACEDNSGLPEEsQFQTWLNAVIPQ--FQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLL 83
Cdd:COG0319    1 MSIEIQNEDDFELDEA-LLERWLEAALEAegLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPLL 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 226710479  84 GDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEAIETEIMLALGYED 148
Cdd:COG0319   80 GDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 6-148 3.16e-55

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: 170.34  E-value: 3.16e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479   6 LDLQLACEDNSGLPEEsQFQTWLNAVIPQ--FQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLL 83
Cdd:COG0319    1 MSIEIQNEDDFELDEA-LLERWLEAALEAegLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPLL 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 226710479  84 GDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEAIETEIMLALGYED 148
Cdd:COG0319   80 GDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
PRK13963 PRK13963
rRNA maturation RNase YbeY;
6-150 1.35e-48

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 157.25  E-value: 1.35e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479   6 LDLQ----LACEDNSGLPEESQFQTWLNaviPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPF-EVPPGmem 80
Cdd:PRK13963 114 LTVQygdeIGGAQRKALPKRKLIAEWIE---PALFADAQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYaEEPDG--- 187

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479  81 SLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEAIETEIMLALGYEDPY 150
Cdd:PRK13963 188 PVIGDLVLCCPVVEKEAREQGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLGFPNPY 257
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 19-144 1.88e-41

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: 134.52  E-value: 1.88e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479   19 PEESQFQTWLNAVI--PQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPgmemSLLGDLVICRQVVEKE 96
Cdd:pfam02130   2 DYEKLIKLVLEAALdeEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPE----EPLGDIVISPEKAKEQ 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 226710479   97 AQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEAIETEIMLAL 144
Cdd:pfam02130  78 AEEYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 40-145 1.43e-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: 126.99  E-value: 1.43e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479   40 EVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFE---VPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGS 116
Cdd:TIGR00043   2 ELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEeeePPGGFPEEVLGDIVISLEVAKEQAKEYGHSLERELAHLTVHGL 81

                          90       100
                  ....*....|....*....|....*....
gi 226710479  117 LHLLGYDHIEDDEAEEMEAIETEIMLALG 145
Cdd:TIGR00043  82 LHLLGYDHETEDEEKEMFALEEEILALLG 110
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 6-148 3.16e-55

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: 170.34  E-value: 3.16e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479   6 LDLQLACEDNSGLPEEsQFQTWLNAVIPQ--FQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLL 83
Cdd:COG0319    1 MSIEIQNEDDFELDEA-LLERWLEAALEAegLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPLL 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 226710479  84 GDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEAIETEIMLALGYED 148
Cdd:COG0319   80 GDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
PRK13963 PRK13963
rRNA maturation RNase YbeY;
6-150 1.35e-48

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 157.25  E-value: 1.35e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479   6 LDLQ----LACEDNSGLPEESQFQTWLNaviPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPF-EVPPGmem 80
Cdd:PRK13963 114 LTVQygdeIGGAQRKALPKRKLIAEWIE---PALFADAQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYaEEPDG--- 187

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479  81 SLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEAIETEIMLALGYEDPY 150
Cdd:PRK13963 188 PVIGDLVLCCPVVEKEAREQGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLGFPNPY 257
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 19-144 1.88e-41

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: 134.52  E-value: 1.88e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479   19 PEESQFQTWLNAVI--PQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPgmemSLLGDLVICRQVVEKE 96
Cdd:pfam02130   2 DYEKLIKLVLEAALdeEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPE----EPLGDIVISPEKAKEQ 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 226710479   97 AQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEAIETEIMLAL 144
Cdd:pfam02130  78 AEEYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 40-145 1.43e-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: 126.99  E-value: 1.43e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479   40 EVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFE---VPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGS 116
Cdd:TIGR00043   2 ELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEeeePPGGFPEEVLGDIVISLEVAKEQAKEYGHSLERELAHLTVHGL 81

                          90       100
                  ....*....|....*....|....*....
gi 226710479  117 LHLLGYDHIEDDEAEEMEAIETEIMLALG 145
Cdd:TIGR00043  82 LHLLGYDHETEDEEKEMFALEEEILALLG 110
PLN02887 PLN02887
hydrolase family protein
 54-147 9.33e-10

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 56.04  E-value: 9.33e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226710479  54 LNLTYRGKDKPTNVLSFPFEVPpGMEMS--LLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAE 131
Cdd:PLN02887 175 LNKEWRGEDHATDVLSMSQHVP-GLKLPvlMLGDIVISVETAARQAEERGHTLLDEIRILVVHGLLHLLGFDHEISNEAE 253

                         90
                 ....*....|....*..
gi 226710479 132 EMEAIETEIML-ALGYE 147
Cdd:PLN02887 254 AEMEKEEELLLkSLGWK 270
 
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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