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Conserved domains on  [gi|690757821|gb|KGF06535|]
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endoribonuclease YbeY [Arcanobacterium sp. S3PF19]

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 ...
 2-147 1.63e-53

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: 166.49  E-value: 1.63e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690757821   2 IEVNDESGFvpAVDLAEVSELASRVLAEMRVHPQADLNILFADEDTMEELHIKWLGLPGPTDVMSFPMDELRPSPPGtdp 81
Cdd:COG0319    3 IEIQNEDDF--ELDEALLERWLEAALEAEGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPP--- 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 690757821  82 qpgMLGDIVICPSVAAAQAEKSGHATMEEVLLLATHGILHLLGYDHAEEGERKEMFDLQRRLLLTF 147
Cdd:COG0319   78 ---LLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKL 140
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 2-147 1.63e-53

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: 166.49  E-value: 1.63e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690757821   2 IEVNDESGFvpAVDLAEVSELASRVLAEMRVHPQADLNILFADEDTMEELHIKWLGLPGPTDVMSFPMDELRPSPPGtdp 81
Cdd:COG0319    3 IEIQNEDDF--ELDEALLERWLEAALEAEGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPP--- 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 690757821  82 qpgMLGDIVICPSVAAAQAEKSGHATMEEVLLLATHGILHLLGYDHAEEGERKEMFDLQRRLLLTF 147
Cdd:COG0319   78 ---LLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKL 140
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 16-144 1.90e-44

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: 142.99  E-value: 1.90e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690757821   16 LAEVSELASRVLAEMRVHPQADLNILFADEDTMEELHIKWLGLPGPTDVMSFPMDELRPSppgtdpqpgmLGDIVICPSV 95
Cdd:pfam02130   4 EKLIKLVLEAALDEEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP----------LGDIVISPEK 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 690757821   96 AAAQAEKSGHATMEEVLLLATHGILHLLGYDHAEEGERKEMFDLQRRLL 144
Cdd:pfam02130  74 AKEQAEEYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEIL 122
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 36-144 8.06e-38

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: 125.45  E-value: 8.06e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690757821   36 ADLNILFADEDTMEELHIKWLGLPGPTDVMSFPMDELrpsPPGTDPQPGMLGDIVICPSVAAAQAEKSGHATMEEVLLLA 115
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEE---EPPGGFPEEVLGDIVISLEVAKEQAKEYGHSLERELAHLT 77

                          90       100
                  ....*....|....*....|....*....
gi 690757821  116 THGILHLLGYDHAEEGERKEMFDLQRRLL 144
Cdd:TIGR00043  78 VHGLLHLLGYDHETEDEEKEMFALEEEIL 106
PLN02887 PLN02887
hydrolase family protein
 37-151 2.26e-15

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 72.60  E-value: 2.26e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690757821  37 DLNILFADEDTMEELHIKWLGLPGPTDVMSfpmdeLRPSPPGTDPQPGMLGDIVICPSVAAAQAEKSGHATMEEVLLLAT 116
Cdd:PLN02887 161 ELSVMLCNDDFIRKLNKEWRGEDHATDVLS-----MSQHVPGLKLPVLMLGDIVISVETAARQAEERGHTLLDEIRILVV 235

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 690757821 117 HGILHLLGYDHAEEGERKEMFDLQRRLLLTFLARK 151
Cdd:PLN02887 236 HGLLHLLGFDHEISNEAEAEMEKEEELLLKSLGWK 270
 
Name Accession Description Interval E-value
YbeY COG0319
ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and ...
 2-147 1.63e-53

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: 166.49  E-value: 1.63e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690757821   2 IEVNDESGFvpAVDLAEVSELASRVLAEMRVHPQADLNILFADEDTMEELHIKWLGLPGPTDVMSFPMDELRPSPPGtdp 81
Cdd:COG0319    3 IEIQNEDDF--ELDEALLERWLEAALEAEGLAEDAELSVRFVDDEEIRELNREYRGKDKPTDVLSFPYDELPEDGPP--- 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 690757821  82 qpgMLGDIVICPSVAAAQAEKSGHATMEEVLLLATHGILHLLGYDHAEEGERKEMFDLQRRLLLTF 147
Cdd:COG0319   78 ---LLGDIVISVETAAREAKEQGHSFEDELAHLLVHGLLHLLGYDHETEEEAEEMEALEEEILAKL 140
YbeY pfam02130
Endoribonuclease YbeY; YbeY is a single strand-specific metallo-endoribonuclease involved in ...
 16-144 1.90e-44

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: 142.99  E-value: 1.90e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690757821   16 LAEVSELASRVLAEMRVHPQADLNILFADEDTMEELHIKWLGLPGPTDVMSFPMDELRPSppgtdpqpgmLGDIVICPSV 95
Cdd:pfam02130   4 EKLIKLVLEAALDEEKVPYEAEVSVTFVDNEEIRELNKEYRGKDKPTDVLSFPMDEPEEP----------LGDIVISPEK 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 690757821   96 AAAQAEKSGHATMEEVLLLATHGILHLLGYDHAEEGERKEMFDLQRRLL 144
Cdd:pfam02130  74 AKEQAEEYGHSLERELAFLTVHGLLHLLGYDHEEEEEAKEMEELEEEIL 122
TIGR00043 TIGR00043
rRNA maturation RNase YbeY; This metalloprotein family is represented by a single member ...
 36-144 8.06e-38

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: 125.45  E-value: 8.06e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690757821   36 ADLNILFADEDTMEELHIKWLGLPGPTDVMSFPMDELrpsPPGTDPQPGMLGDIVICPSVAAAQAEKSGHATMEEVLLLA 115
Cdd:TIGR00043   1 GELSLLFVDDEEIQELNREYRDKDYPTDVLSFPYEEE---EPPGGFPEEVLGDIVISLEVAKEQAKEYGHSLERELAHLT 77

                          90       100
                  ....*....|....*....|....*....
gi 690757821  116 THGILHLLGYDHAEEGERKEMFDLQRRLL 144
Cdd:TIGR00043  78 VHGLLHLLGYDHETEDEEKEMFALEEEIL 106
PLN02887 PLN02887
hydrolase family protein
 37-151 2.26e-15

hydrolase family protein


Pssm-ID: 215479 [Multi-domain]  Cd Length: 580  Bit Score: 72.60  E-value: 2.26e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690757821  37 DLNILFADEDTMEELHIKWLGLPGPTDVMSfpmdeLRPSPPGTDPQPGMLGDIVICPSVAAAQAEKSGHATMEEVLLLAT 116
Cdd:PLN02887 161 ELSVMLCNDDFIRKLNKEWRGEDHATDVLS-----MSQHVPGLKLPVLMLGDIVISVETAARQAEERGHTLLDEIRILVV 235

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 690757821 117 HGILHLLGYDHAEEGERKEMFDLQRRLLLTFLARK 151
Cdd:PLN02887 236 HGLLHLLGFDHEISNEAEAEMEKEEELLLKSLGWK 270
PRK13963 PRK13963
rRNA maturation RNase YbeY;
36-136 3.93e-09

rRNA maturation RNase YbeY;


Pssm-ID: 237573  Cd Length: 258  Bit Score: 54.01  E-value: 3.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690757821  36 ADLNILFADEDTMEELHIKWLGLPGPTDVMSFPMDElrpSPPGTdpqpgMLGDIVICPSVAAAQAEKSGHATMEEVLLLA 115
Cdd:PRK13963 148 AQLTVRFVGEEEGRTLNRGYRGKDYATNVLTFAYAE---EPDGP-----VIGDLVLCCPVVEKEAREQGKPLEAHYAHLL 219

                         90       100
                 ....*....|....*....|.
gi 690757821 116 THGILHLLGYDHAEEGERKEM 136
Cdd:PRK13963 220 VHGALHAQGYDHEDDEDAAEM 240
 
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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