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Conserved domains on  [gi|2156716031|ref|WP_230460507|]
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rRNA maturation RNase YbeY [Sansalvadorimonas verongulae]

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 ...
 5-146 2.80e-61

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: 185.36  E-value: 2.80e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2156716031   5 IDLQVagESGNLPSEEQLVAWATAAVRDE--RDEAEISVRIVDVEEGRELNAQWRQKDYATNVLSFPSDLPVELGLPLLG 82
Cdd:COG0319     3 IEIQN--EDDFELDEALLERWLEAALEAEglAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPLLG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2156716031  83 DLVICAPVVEREADEQQKTLTSHWAHMVIHGTLHLLGYDHIEDDEAETMEALETSIMLSLGFND 146
Cdd:COG0319    81 DIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 5-146 2.80e-61

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: 185.36  E-value: 2.80e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2156716031   5 IDLQVagESGNLPSEEQLVAWATAAVRDE--RDEAEISVRIVDVEEGRELNAQWRQKDYATNVLSFPSDLPVELGLPLLG 82
Cdd:COG0319     3 IEIQN--EDDFELDEALLERWLEAALEAEglAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPLLG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2156716031  83 DLVICAPVVEREADEQQKTLTSHWAHMVIHGTLHLLGYDHIEDDEAETMEALETSIMLSLGFND 146
Cdd:COG0319    81 DIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
PRK13963 PRK13963
rRNA maturation RNase YbeY;
10-148 3.25e-52

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 166.49  E-value: 3.25e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2156716031  10 AGESGNLPSEEQLVAWATAAVRDErdeAEISVRIVDVEEGRELNAQWRQKDYATNVLSFPSDlpVELGLPLLGDLVICAP 89
Cdd:PRK13963  124 GAQRKALPKRKLIAEWIEPALFAD---AQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYA--EEPDGPVIGDLVLCCP 198

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2156716031  90 VVEREADEQQKTLTSHWAHMVIHGTLHLLGYDHIEDDEAETMEALETSIMLSLGFNDPY 148
Cdd:PRK13963  199 VVEKEAREQGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLGFPNPY 257
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 21-142 2.57e-45

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: 144.53  E-value: 2.57e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2156716031  21 QLVAWATAAVRDERDEAEISVRIVDVEEGRELNAQWRQKDYATNVLSFPSDLPVELglplLGDLVICAPVVEREADEQQK 100
Cdd:pfam02130   8 KLVLEAALDEEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP----LGDIVISPEKAKEQAEEYGH 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2156716031 101 TLTSHWAHMVIHGTLHLLGYDHIEDDEAETMEALETSIMLSL 142
Cdd:pfam02130  84 SLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 37-143 2.82e-43

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: 138.93  E-value: 2.82e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2156716031  37 AEISVRIVDVEEGRELNAQWRQKDYATNVLSFPS---DLPVELGLPLLGDLVICAPVVEREADEQQKTLTSHWAHMVIHG 113
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYeeeEPPGGFPEEVLGDIVISLEVAKEQAKEYGHSLERELAHLTVHG 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2156716031 114 TLHLLGYDHIEDDEAETMEALETSIMLSLG 143
Cdd:TIGR00043  81 LLHLLGYDHETEDEEKEMFALEEEILALLG 110
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 5-146 2.80e-61

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: 185.36  E-value: 2.80e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2156716031   5 IDLQVagESGNLPSEEQLVAWATAAVRDE--RDEAEISVRIVDVEEGRELNAQWRQKDYATNVLSFPSDLPVELGLPLLG 82
Cdd:COG0319     3 IEIQN--EDDFELDEALLERWLEAALEAEglAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPPLLG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2156716031  83 DLVICAPVVEREADEQQKTLTSHWAHMVIHGTLHLLGYDHIEDDEAETMEALETSIMLSLGFND 146
Cdd:COG0319    81 DIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
PRK13963 PRK13963
rRNA maturation RNase YbeY;
10-148 3.25e-52

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 166.49  E-value: 3.25e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2156716031  10 AGESGNLPSEEQLVAWATAAVRDErdeAEISVRIVDVEEGRELNAQWRQKDYATNVLSFPSDlpVELGLPLLGDLVICAP 89
Cdd:PRK13963  124 GAQRKALPKRKLIAEWIEPALFAD---AQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYA--EEPDGPVIGDLVLCCP 198

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2156716031  90 VVEREADEQQKTLTSHWAHMVIHGTLHLLGYDHIEDDEAETMEALETSIMLSLGFNDPY 148
Cdd:PRK13963  199 VVEKEAREQGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLGFPNPY 257
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 21-142 2.57e-45

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: 144.53  E-value: 2.57e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2156716031  21 QLVAWATAAVRDERDEAEISVRIVDVEEGRELNAQWRQKDYATNVLSFPSDLPVELglplLGDLVICAPVVEREADEQQK 100
Cdd:pfam02130   8 KLVLEAALDEEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP----LGDIVISPEKAKEQAEEYGH 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2156716031 101 TLTSHWAHMVIHGTLHLLGYDHIEDDEAETMEALETSIMLSL 142
Cdd:pfam02130  84 SLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 37-143 2.82e-43

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: 138.93  E-value: 2.82e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2156716031  37 AEISVRIVDVEEGRELNAQWRQKDYATNVLSFPS---DLPVELGLPLLGDLVICAPVVEREADEQQKTLTSHWAHMVIHG 113
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYeeeEPPGGFPEEVLGDIVISLEVAKEQAKEYGHSLERELAHLTVHG 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2156716031 114 TLHLLGYDHIEDDEAETMEALETSIMLSLG 143
Cdd:TIGR00043  81 LLHLLGYDHETEDEEKEMFALEEEILALLG 110
PLN02887 PLN02887
hydrolase family protein
 35-144 8.65e-19

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 81.84  E-value: 8.65e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2156716031  35 DEAEISVRIVDVEEGRELNAQWRQKDYATNVLSFPSDLPvELGLP--LLGDLVICAPVVEREADEQQKTLTSHWAHMVIH 112
Cdd:PLN02887  158 DSVELSVMLCNDDFIRKLNKEWRGEDHATDVLSMSQHVP-GLKLPvlMLGDIVISVETAARQAEERGHTLLDEIRILVVH 236

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2156716031 113 GTLHLLGYDHIEDDEAET-MEALETSIMLSLGF 144
Cdd:PLN02887  237 GLLHLLGFDHEISNEAEAeMEKEEELLLKSLGW 269
 
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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