NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|752685848|ref|WP_041333780|]
View 

MULTISPECIES: rRNA maturation RNase YbeY [Bacillus]

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 ...
 1-156 1.02e-58

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: 179.20  E-value: 1.02e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752685848   1 MSLLIDIVDETgSVSEEmlkEVENLLQFAAEREGVQDQAEVSVTIVSNDDIHQINKEYRGKDAPTDVISFALEEEGegei 80
Cdd:COG0319    1 MSIEIQNEDDF-ELDEA---LLERWLEAALEAEGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELP---- 72

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 752685848  81 eivgAEMPPVLGDIIISADRTREQAEEYNHSFKRELGFLAVHGFLHLLGYDHLTKEEEEEMFTKQKELLDAYGLKR 156
Cdd:COG0319   73 ----EDGPPLLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 1-156 1.02e-58

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: 179.20  E-value: 1.02e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752685848   1 MSLLIDIVDETgSVSEEmlkEVENLLQFAAEREGVQDQAEVSVTIVSNDDIHQINKEYRGKDAPTDVISFALEEEGegei 80
Cdd:COG0319    1 MSIEIQNEDDF-ELDEA---LLERWLEAALEAEGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELP---- 72

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 752685848  81 eivgAEMPPVLGDIIISADRTREQAEEYNHSFKRELGFLAVHGFLHLLGYDHLTKEEEEEMFTKQKELLDAYGLKR 156
Cdd:COG0319   73 ----EDGPPLLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 16-152 1.09e-58

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: 178.43  E-value: 1.09e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752685848   16 EEMLKEVENLLQFAAEREGVQDQAEVSVTIVSNDDIHQINKEYRGKDAPTDVISFALEeegegeieivgaEMPPVLGDII 95
Cdd:pfam02130   1 IDYEKLIKLVLEAALDEEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMD------------EPEEPLGDIV 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 752685848   96 ISADRTREQAEEYNHSFKRELGFLAVHGFLHLLGYDHLTKEEEEEMFTKQKELLDAY 152
Cdd:pfam02130  69 ISPEKAKEQAEEYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 39-153 5.34e-45

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: 143.17  E-value: 5.34e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752685848   39 AEVSVTIVSNDDIHQINKEYRGKDAPTDVISFALEEEGEgeieiVGAEMPPVLGDIIISADRTREQAEEYNHSFKRELGF 118
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEP-----PGGFPEEVLGDIVISLEVAKEQAKEYGHSLERELAH 75

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 752685848  119 LAVHGFLHLLGYDHLTKEEEEEMFTKQKELLDAYG 153
Cdd:TIGR00043  76 LTVHGLLHLLGYDHETEDEEKEMFALEEEILALLG 110
PLN02887 PLN02887
hydrolase family protein
 34-149 5.05e-19

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 82.61  E-value: 5.05e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752685848  34 GVQDQAEVSVTIVSNDDIHQINKEYRGKDAPTDVISFAleeegegeIEIVGAEMPPV-LGDIIISADRTREQAEEYNHSF 112
Cdd:PLN02887 155 GGYDSVELSVMLCNDDFIRKLNKEWRGEDHATDVLSMS--------QHVPGLKLPVLmLGDIVISVETAARQAEERGHTL 226

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 752685848 113 KRELGFLAVHGFLHLLGYDHLTKEEEEEMFTKQKELL 149
Cdd:PLN02887 227 LDEIRILVVHGLLHLLGFDHEISNEAEAEMEKEEELL 263
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 1-156 1.02e-58

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: 179.20  E-value: 1.02e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752685848   1 MSLLIDIVDETgSVSEEmlkEVENLLQFAAEREGVQDQAEVSVTIVSNDDIHQINKEYRGKDAPTDVISFALEEEGegei 80
Cdd:COG0319    1 MSIEIQNEDDF-ELDEA---LLERWLEAALEAEGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELP---- 72

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 752685848  81 eivgAEMPPVLGDIIISADRTREQAEEYNHSFKRELGFLAVHGFLHLLGYDHLTKEEEEEMFTKQKELLDAYGLKR 156
Cdd:COG0319   73 ----EDGPPLLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 16-152 1.09e-58

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: 178.43  E-value: 1.09e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752685848   16 EEMLKEVENLLQFAAEREGVQDQAEVSVTIVSNDDIHQINKEYRGKDAPTDVISFALEeegegeieivgaEMPPVLGDII 95
Cdd:pfam02130   1 IDYEKLIKLVLEAALDEEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMD------------EPEEPLGDIV 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 752685848   96 ISADRTREQAEEYNHSFKRELGFLAVHGFLHLLGYDHLTKEEEEEMFTKQKELLDAY 152
Cdd:pfam02130  69 ISPEKAKEQAEEYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 39-153 5.34e-45

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: 143.17  E-value: 5.34e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752685848   39 AEVSVTIVSNDDIHQINKEYRGKDAPTDVISFALEEEGEgeieiVGAEMPPVLGDIIISADRTREQAEEYNHSFKRELGF 118
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEP-----PGGFPEEVLGDIVISLEVAKEQAKEYGHSLERELAH 75

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 752685848  119 LAVHGFLHLLGYDHLTKEEEEEMFTKQKELLDAYG 153
Cdd:TIGR00043  76 LTVHGLLHLLGYDHETEDEEKEMFALEEEILALLG 110
PLN02887 PLN02887
hydrolase family protein
 34-149 5.05e-19

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 82.61  E-value: 5.05e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752685848  34 GVQDQAEVSVTIVSNDDIHQINKEYRGKDAPTDVISFAleeegegeIEIVGAEMPPV-LGDIIISADRTREQAEEYNHSF 112
Cdd:PLN02887 155 GGYDSVELSVMLCNDDFIRKLNKEWRGEDHATDVLSMS--------QHVPGLKLPVLmLGDIVISVETAARQAEERGHTL 226

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 752685848 113 KRELGFLAVHGFLHLLGYDHLTKEEEEEMFTKQKELL 149
Cdd:PLN02887 227 LDEIRILVVHGLLHLLGFDHEISNEAEAEMEKEEELL 263
PRK13963 PRK13963
rRNA maturation RNase YbeY;
39-153 4.06e-14

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 67.50  E-value: 4.06e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752685848  39 AEVSVTIVSNDDIHQINKEYRGKDAPTDVISFALeeegegeieivgAEMP--PVLGDIIISADRTREQAEEYNHSFKREL 116
Cdd:PRK13963 148 AQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAY------------AEEPdgPVIGDLVLCCPVVEKEAREQGKPLEAHY 215

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 752685848 117 GFLAVHGFLHLLGYDHLTKEEEEEMFTKQKELLDAYG 153
Cdd:PRK13963 216 AHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLG 252
 
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