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Conserved domains on  [gi|996844910|emb|CXO90298|]
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metal-dependent hydrolase [Staphylococcus aureus]

Protein Classification

rRNA maturation RNAse YbeY( domain architecture ID 10489333)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 19-150 6.23e-59

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: 178.82  E-value: 6.23e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996844910   19 KQIEDLLEFAKKEEHIEDDAELSVTFVDKQEIQEINRTYRDKDKVTDVISFALEEDEPEidfsdldiprvLGDIIICTDV 98
Cdd:pfam02130   5 KLIKLVLEAALDEEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP-----------LGDIVISPEK 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 996844910   99 AQEQANNYGHSFERELGFLALHGFLHLLGYDHMTEADEKEMFGRQDTILNAY 150
Cdd:pfam02130  74 AKEQAEEYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
 
Name Accession Description Interval E-value
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 19-150 6.23e-59

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: 178.82  E-value: 6.23e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996844910   19 KQIEDLLEFAKKEEHIEDDAELSVTFVDKQEIQEINRTYRDKDKVTDVISFALEEDEPEidfsdldiprvLGDIIICTDV 98
Cdd:pfam02130   5 KLIKLVLEAALDEEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP-----------LGDIVISPEK 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 996844910   99 AQEQANNYGHSFERELGFLALHGFLHLLGYDHMTEADEKEMFGRQDTILNAY 150
Cdd:pfam02130  74 AKEQAEEYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 3-154 4.76e-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: 177.27  E-value: 4.76e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996844910   3 TIDFSDHTGlvKDAWYKQIEDLLEFAKKEEHIEDDAELSVTFVDKQEIQEINRTYRDKDKVTDVISFALEEDEPeidfsd 82
Cdd:COG0319    2 SIEIQNEDD--FELDEALLERWLEAALEAEGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPE------ 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 996844910  83 lDIPRVLGDIIICTDVAQEQANNYGHSFERELGFLALHGFLHLLGYDHMTEADEKEMFGRQDTILNAYGLTR 154
Cdd:COG0319   74 -DGPPLLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 38-151 7.62e-47

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: 147.79  E-value: 7.62e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996844910   38 AELSVTFVDKQEIQEINRTYRDKDKVTDVISFALEEDEPEIDFSdldiPRVLGDIIICTDVAQEQANNYGHSFERELGFL 117
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGGFP----EEVLGDIVISLEVAKEQAKEYGHSLERELAHL 76

                          90       100       110
                  ....*....|....*....|....*....|....
gi 996844910  118 ALHGFLHLLGYDHMTEADEKEMFGRQDTILNAYG 151
Cdd:TIGR00043  77 TVHGLLHLLGYDHETEDEEKEMFALEEEILALLG 110
PRK13963 PRK13963
rRNA maturation RNase YbeY;
19-151 4.12e-23

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 91.38  E-value: 4.12e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996844910  19 KQIEDLLEFAkkeehIEDDAELSVTFVDKQEIQEINRTYRDKDKVTDVISFALEEDEpeidfsdlDIPrVLGDIIICTDV 98
Cdd:PRK13963 134 KLIAEWIEPA-----LFADAQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYAEEP--------DGP-VIGDLVLCCPV 199

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 996844910  99 AQEQANNYGHSFERELGFLALHGFLHLLGYDHMTEADEKEMFGRQDTILNAYG 151
Cdd:PRK13963 200 VEKEAREQGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLG 252
 
Name Accession Description Interval E-value
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 19-150 6.23e-59

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: 178.82  E-value: 6.23e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996844910   19 KQIEDLLEFAKKEEHIEDDAELSVTFVDKQEIQEINRTYRDKDKVTDVISFALEEDEPEidfsdldiprvLGDIIICTDV 98
Cdd:pfam02130   5 KLIKLVLEAALDEEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP-----------LGDIVISPEK 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 996844910   99 AQEQANNYGHSFERELGFLALHGFLHLLGYDHMTEADEKEMFGRQDTILNAY 150
Cdd:pfam02130  74 AKEQAEEYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEILNKL 125
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 3-154 4.76e-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: 177.27  E-value: 4.76e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996844910   3 TIDFSDHTGlvKDAWYKQIEDLLEFAKKEEHIEDDAELSVTFVDKQEIQEINRTYRDKDKVTDVISFALEEDEPeidfsd 82
Cdd:COG0319    2 SIEIQNEDD--FELDEALLERWLEAALEAEGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPE------ 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 996844910  83 lDIPRVLGDIIICTDVAQEQANNYGHSFERELGFLALHGFLHLLGYDHMTEADEKEMFGRQDTILNAYGLTR 154
Cdd:COG0319   74 -DGPPLLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKLGIPD 144
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 38-151 7.62e-47

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: 147.79  E-value: 7.62e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996844910   38 AELSVTFVDKQEIQEINRTYRDKDKVTDVISFALEEDEPEIDFSdldiPRVLGDIIICTDVAQEQANNYGHSFERELGFL 117
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEEEPPGGFP----EEVLGDIVISLEVAKEQAKEYGHSLERELAHL 76

                          90       100       110
                  ....*....|....*....|....*....|....
gi 996844910  118 ALHGFLHLLGYDHMTEADEKEMFGRQDTILNAYG 151
Cdd:TIGR00043  77 TVHGLLHLLGYDHETEDEEKEMFALEEEILALLG 110
PRK13963 PRK13963
rRNA maturation RNase YbeY;
19-151 4.12e-23

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 91.38  E-value: 4.12e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996844910  19 KQIEDLLEFAkkeehIEDDAELSVTFVDKQEIQEINRTYRDKDKVTDVISFALEEDEpeidfsdlDIPrVLGDIIICTDV 98
Cdd:PRK13963 134 KLIAEWIEPA-----LFADAQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYAEEP--------DGP-VIGDLVLCCPV 199

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 996844910  99 AQEQANNYGHSFERELGFLALHGFLHLLGYDHMTEADEKEMFGRQDTILNAYG 151
Cdd:PRK13963 200 VEKEAREQGKPLEAHYAHLLVHGALHAQGYDHEDDEDAAEMEALETDILAKLG 252
PLN02887 PLN02887
hydrolase family protein
 13-151 5.44e-17

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 76.84  E-value: 5.44e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996844910  13 VKDAWYK----QIEDLLEFakkeehieDDAELSVTFVDKQEIQEINRTYRDKDKVTDVISfaLEEDEPEIDFSDLdiprV 88
Cdd:PLN02887 139 LKDSKYKtrdtDISDVGGY--------DSVELSVMLCNDDFIRKLNKEWRGEDHATDVLS--MSQHVPGLKLPVL----M 204

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 996844910  89 LGDIIICTDVAQEQANNYGHSFERELGFLALHGFLHLLGYDH-MTEADEKEMFGRQDTILNAYG 151
Cdd:PLN02887 205 LGDIVISVETAARQAEERGHTLLDEIRILVVHGLLHLLGFDHeISNEAEAEMEKEEELLLKSLG 268
 
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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