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Conserved domains on  [gi|757600731|ref|WP_042848341|]
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MULTISPECIES: rRNA maturation RNase YbeY [Providencia]

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 ...
 6-150 1.19e-64

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: 194.22  E-value: 1.19e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757600731   6 IILDLQIACENPdglPSEALFERWLAAVLP--KFQAQSEVTIRIVDEAESHHLNLTYRGKDKPTNVLSFPFEAPPEIELP 83
Cdd:COG0319    1 MSIEIQNEDDFE---LDEALLERWLEAALEaeGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPP 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 757600731  84 LLGDLIICRQVVEQEAIEQQKSAEEHWAHMVIHGCLHLLGYDHIEDDEAEEMESLETEILAELGYDD 150
Cdd:COG0319   78 LLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 6-150 1.19e-64

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: 194.22  E-value: 1.19e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757600731   6 IILDLQIACENPdglPSEALFERWLAAVLP--KFQAQSEVTIRIVDEAESHHLNLTYRGKDKPTNVLSFPFEAPPEIELP 83
Cdd:COG0319    1 MSIEIQNEDDFE---LDEALLERWLEAALEaeGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPP 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 757600731  84 LLGDLIICRQVVEQEAIEQQKSAEEHWAHMVIHGCLHLLGYDHIEDDEAEEMESLETEILAELGYDD 150
Cdd:COG0319   78 LLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
PRK13963 PRK13963
rRNA maturation RNase YbeY;
19-152 1.17e-52

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 167.65  E-value: 1.17e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757600731  19 GLPSEALFERWLAAVLpkfQAQSEVTIRIVDEAESHHLNLTYRGKDKPTNVLSFPFEAPPEIelPLLGDLIICRQVVEQE 98
Cdd:PRK13963 129 ALPKRKLIAEWIEPAL---FADAQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYAEEPDG--PVIGDLVLCCPVVEKE 203

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 757600731  99 AIEQQKSAEEHWAHMVIHGCLHLLGYDHIEDDEAEEMESLETEILAELGYDDPY 152
Cdd:PRK13963 204 AREQGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLGFPNPY 257
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 23-146 4.98e-50

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: 156.48  E-value: 4.98e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757600731   23 EALFERWLAAVL--PKFQAQSEVTIRIVDEAESHHLNLTYRGKDKPTNVLSFPFEAPPEIelplLGDLIICRQVVEQEAI 100
Cdd:pfam02130   4 EKLIKLVLEAALdeEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP----LGDIVISPEKAKEQAE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 757600731  101 EQQKSAEEHWAHMVIHGCLHLLGYDHIEDDEAEEMESLETEILAEL 146
Cdd:pfam02130  80 EYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 42-147 2.03e-44

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: 141.63  E-value: 2.03e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757600731   42 EVTIRIVDEAESHHLNLTYRGKDKPTNVLSFPFEAPPEIELP---LLGDLIICRQVVEQEAIEQQKSAEEHWAHMVIHGC 118
Cdd:TIGR00043   2 ELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGGFpeeVLGDIVISLEVAKEQAKEYGHSLERELAHLTVHGL 81

                          90       100
                  ....*....|....*....|....*....
gi 757600731  119 LHLLGYDHIEDDEAEEMESLETEILAELG 147
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 ...
 6-150 1.19e-64

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: 194.22  E-value: 1.19e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757600731   6 IILDLQIACENPdglPSEALFERWLAAVLP--KFQAQSEVTIRIVDEAESHHLNLTYRGKDKPTNVLSFPFEAPPEIELP 83
Cdd:COG0319    1 MSIEIQNEDDFE---LDEALLERWLEAALEaeGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPP 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 757600731  84 LLGDLIICRQVVEQEAIEQQKSAEEHWAHMVIHGCLHLLGYDHIEDDEAEEMESLETEILAELGYDD 150
Cdd:COG0319   78 LLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
PRK13963 PRK13963
rRNA maturation RNase YbeY;
19-152 1.17e-52

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 167.65  E-value: 1.17e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757600731  19 GLPSEALFERWLAAVLpkfQAQSEVTIRIVDEAESHHLNLTYRGKDKPTNVLSFPFEAPPEIelPLLGDLIICRQVVEQE 98
Cdd:PRK13963 129 ALPKRKLIAEWIEPAL---FADAQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYAEEPDG--PVIGDLVLCCPVVEKE 203

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 757600731  99 AIEQQKSAEEHWAHMVIHGCLHLLGYDHIEDDEAEEMESLETEILAELGYDDPY 152
Cdd:PRK13963 204 AREQGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLGFPNPY 257
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 23-146 4.98e-50

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: 156.48  E-value: 4.98e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757600731   23 EALFERWLAAVL--PKFQAQSEVTIRIVDEAESHHLNLTYRGKDKPTNVLSFPFEAPPEIelplLGDLIICRQVVEQEAI 100
Cdd:pfam02130   4 EKLIKLVLEAALdeEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP----LGDIVISPEKAKEQAE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 757600731  101 EQQKSAEEHWAHMVIHGCLHLLGYDHIEDDEAEEMESLETEILAEL 146
Cdd:pfam02130  80 EYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 42-147 2.03e-44

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: 141.63  E-value: 2.03e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757600731   42 EVTIRIVDEAESHHLNLTYRGKDKPTNVLSFPFEAPPEIELP---LLGDLIICRQVVEQEAIEQQKSAEEHWAHMVIHGC 118
Cdd:TIGR00043   2 ELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGGFpeeVLGDIVISLEVAKEQAKEYGHSLERELAHLTVHGL 81

                          90       100
                  ....*....|....*....|....*....
gi 757600731  119 LHLLGYDHIEDDEAEEMESLETEILAELG 147
Cdd:TIGR00043  82 LHLLGYDHETEDEEKEMFALEEEILALLG 110
PLN02887 PLN02887
hydrolase family protein
 56-157 8.78e-13

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 64.51  E-value: 8.78e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 757600731  56 LNLTYRGKDKPTNVLSFPfEAPPEIELP--LLGDLIICRQVVEQEAIEQQKSAEEHWAHMVIHGCLHLLGYDHIEDDEAE 133
Cdd:PLN02887 175 LNKEWRGEDHATDVLSMS-QHVPGLKLPvlMLGDIVISVETAARQAEERGHTLLDEIRILVVHGLLHLLGFDHEISNEAE 253

                         90       100
                 ....*....|....*....|....*
gi 757600731 134 -EMESLETEILAELGYDDPYLAEKA 157
Cdd:PLN02887 254 aEMEKEEELLLKSLGWKGKGLIQSA 278
 
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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