NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|488940589|ref|WP_002851664|]
View 

MULTISPECIES: rRNA maturation RNase YbeY [Campylobacter]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 19-125 4.04e-36

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: 121.03  E-value: 4.04e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488940589  19 SPKDVELVFVDSKEMQEINLEQRKQDKTTDVLSFPLENI--DESLPLGSVVINVDLAKEKAKELGHSYEEEISLLFIHAM 96
Cdd:COG0319   33 EDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELpeDGPPLLGDIVISVETAAREAKEQGHSFEDELAHLLVHGL 112

                         90       100       110
                 ....*....|....*....|....*....|.
gi 488940589  97 LHLLGFDHENDN--GEMREKEKELIEHFNLP 125
Cdd:COG0319  113 LHLLGYDHETEEeaEEMEALEEEILAKLGIP 143
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 19-125 4.04e-36

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: 121.03  E-value: 4.04e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488940589  19 SPKDVELVFVDSKEMQEINLEQRKQDKTTDVLSFPLENI--DESLPLGSVVINVDLAKEKAKELGHSYEEEISLLFIHAM 96
Cdd:COG0319   33 EDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELpeDGPPLLGDIVISVETAAREAKEQGHSFEDELAHLLVHGL 112

                         90       100       110
                 ....*....|....*....|....*....|.
gi 488940589  97 LHLLGFDHENDN--GEMREKEKELIEHFNLP 125
Cdd:COG0319  113 LHLLGYDHETEEeaEEMEALEEEILAKLGIP 143
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 21-123 4.08e-36

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: 119.67  E-value: 4.08e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488940589   21 KDVELVFVDSKEMQEINLEQRKQDKTTDVLSFPLENIDE-----SLPLGSVVINVDLAKEKAKELGHSYEEEISLLFIHA 95
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPpggfpEEVLGDIVISLEVAKEQAKEYGHSLERELAHLTVHG 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 488940589   96 MLHLLGFDHENDNGE--MREKEKELIEHFN 123
Cdd:TIGR00043  81 LLHLLGYDHETEDEEkeMFALEEEILALLG 110
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 23-122 5.53e-36

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: 119.88  E-value: 5.53e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488940589   23 VELVFVDSKEMQEINLEQRKQDKTTDVLSFPLENIDEslPLGSVVINVDLAKEKAKELGHSYEEEISLLFIHAMLHLLGF 102
Cdd:pfam02130  26 VSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEE--PLGDIVISPEKAKEQAEEYGHSLERELAFLTVHGLLHLLGY 103

                          90       100
                  ....*....|....*....|..
gi 488940589  103 DHENDN--GEMREKEKELIEHF 122
Cdd:pfam02130 104 DHEEEEeaKEMEELEEEILNKL 125
PLN02887 PLN02887
hydrolase family protein
 33-117 8.92e-16

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 72.60  E-value: 8.92e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488940589  33 MQEINLEQRKQDKTTDVLSFPLENIDESLP---LGSVVINVDLAKEKAKELGHSYEEEISLLFIHAMLHLLGFDHENDNG 109
Cdd:PLN02887 172 IRKLNKEWRGEDHATDVLSMSQHVPGLKLPvlmLGDIVISVETAARQAEERGHTLLDEIRILVVHGLLHLLGFDHEISNE 251


                 ....*...
gi 488940589 110 EMREKEKE 117
Cdd:PLN02887 252 AEAEMEKE 259
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 19-125 4.04e-36

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: 121.03  E-value: 4.04e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488940589  19 SPKDVELVFVDSKEMQEINLEQRKQDKTTDVLSFPLENI--DESLPLGSVVINVDLAKEKAKELGHSYEEEISLLFIHAM 96
Cdd:COG0319   33 EDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELpeDGPPLLGDIVISVETAAREAKEQGHSFEDELAHLLVHGL 112

                         90       100       110
                 ....*....|....*....|....*....|.
gi 488940589  97 LHLLGFDHENDN--GEMREKEKELIEHFNLP 125
Cdd:COG0319  113 LHLLGYDHETEEeaEEMEALEEEILAKLGIP 143
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 21-123 4.08e-36

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: 119.67  E-value: 4.08e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488940589   21 KDVELVFVDSKEMQEINLEQRKQDKTTDVLSFPLENIDE-----SLPLGSVVINVDLAKEKAKELGHSYEEEISLLFIHA 95
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPpggfpEEVLGDIVISLEVAKEQAKEYGHSLERELAHLTVHG 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 488940589   96 MLHLLGFDHENDNGE--MREKEKELIEHFN 123
Cdd:TIGR00043  81 LLHLLGYDHETEDEEkeMFALEEEILALLG 110
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 23-122 5.53e-36

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: 119.88  E-value: 5.53e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488940589   23 VELVFVDSKEMQEINLEQRKQDKTTDVLSFPLENIDEslPLGSVVINVDLAKEKAKELGHSYEEEISLLFIHAMLHLLGF 102
Cdd:pfam02130  26 VSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEE--PLGDIVISPEKAKEQAEEYGHSLERELAFLTVHGLLHLLGY 103

                          90       100
                  ....*....|....*....|..
gi 488940589  103 DHENDN--GEMREKEKELIEHF 122
Cdd:pfam02130 104 DHEEEEeaKEMEELEEEILNKL 125
PLN02887 PLN02887
hydrolase family protein
 33-117 8.92e-16

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 72.60  E-value: 8.92e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488940589  33 MQEINLEQRKQDKTTDVLSFPLENIDESLP---LGSVVINVDLAKEKAKELGHSYEEEISLLFIHAMLHLLGFDHENDNG 109
Cdd:PLN02887 172 IRKLNKEWRGEDHATDVLSMSQHVPGLKLPvlmLGDIVISVETAARQAEERGHTLLDEIRILVVHGLLHLLGFDHEISNE 251


                 ....*...
gi 488940589 110 EMREKEKE 117
Cdd:PLN02887 252 AEAEMEKE 259
PRK13963 PRK13963
rRNA maturation RNase YbeY;
14-120 4.48e-10

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 55.55  E-value: 4.48e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488940589  14 IASFLSP---KDVELV--FVDSKEMQEINLEQRKQDKTTDVLSFPLENIDESLPLGSVVINVDLAKEKAKELGHSYEEEI 88
Cdd:PRK13963 136 IAEWIEPalfADAQLTvrFVGEEEGRTLNRGYRGKDYATNVLTFAYAEEPDGPVIGDLVLCCPVVEKEAREQGKPLEAHY 215

                         90       100       110
                 ....*....|....*....|....*....|..
gi 488940589  89 SLLFIHAMLHLLGFDHENDNgemREKEKELIE 120
Cdd:PRK13963 216 AHLLVHGALHAQGYDHEDDE---DAAEMEALE 244
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH