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Conserved domains on  [gi|21387129|gb|AAM47968|]
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unknown protein [Arabidopsis thaliana]

Protein Classification

YhbY family RNA-binding protein( domain architecture ID 10661237)

YhbY family RNA-binding protein similar to Arabidopsis thaliana CRS2-associated factors and CRM-domain containing factors

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 203-286 7.39e-21

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


:

Pssm-ID: 198171  Cd Length: 84  Bit Score: 86.75  E-value: 7.39e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21387129    203 LKRWEKGMLIKPHMHDNRQVNLGRDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEKTGGEIIHRVGGVV 282
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQVIGKTI 80


                   ....
gi 21387129    283 YLFR 286
Cdd:smart01103  81 VLYR 84
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 321-404 5.05e-19

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


:

Pssm-ID: 198171  Cd Length: 84  Bit Score: 81.74  E-value: 5.05e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21387129    321 LTKEEAHEFRVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVPCVLLSFDDEQI 400
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQVIGKTI 80


                   ....
gi 21387129    401 LMWR 404
Cdd:smart01103  81 VLYR 84
 
Name Accession Description Interval E-value
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 203-286 7.39e-21

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 86.75  E-value: 7.39e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21387129    203 LKRWEKGMLIKPHMHDNRQVNLGRDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEKTGGEIIHRVGGVV 282
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQVIGKTI 80


                   ....
gi 21387129    283 YLFR 286
Cdd:smart01103  81 VLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 207-286 7.30e-20

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 83.99  E-value: 7.30e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21387129   207 EKGMLIKPHMHDNRQVNLGRDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEKTGGEIIHRVGGVVYLFR 286
Cdd:pfam01985   5 ERRYLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKVLKNCREDRKEIAEELAEKTGAEVVQVIGRTIVLYR 84
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 321-404 5.05e-19

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 81.74  E-value: 5.05e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21387129    321 LTKEEAHEFRVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVPCVLLSFDDEQI 400
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQVIGKTI 80


                   ....
gi 21387129    401 LMWR 404
Cdd:smart01103  81 VLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 321-404 7.53e-17

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 75.51  E-value: 7.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21387129   321 LTKEEAHEFRVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVPCVLLSFDDEQI 400
Cdd:pfam01985   1 LTSKERRYLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKVLKNCREDRKEIAEELAEKTGAEVVQVIGRTI 80


                  ....
gi 21387129   401 LMWR 404
Cdd:pfam01985  81 VLYR 84
 
Name Accession Description Interval E-value
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 203-286 7.39e-21

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 86.75  E-value: 7.39e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21387129    203 LKRWEKGMLIKPHMHDNRQVNLGRDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEKTGGEIIHRVGGVV 282
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQVIGKTI 80


                   ....
gi 21387129    283 YLFR 286
Cdd:smart01103  81 VLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 207-286 7.30e-20

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 83.99  E-value: 7.30e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21387129   207 EKGMLIKPHMHDNRQVNLGRDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEKTGGEIIHRVGGVVYLFR 286
Cdd:pfam01985   5 ERRYLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKVLKNCREDRKEIAEELAEKTGAEVVQVIGRTIVLYR 84
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 321-404 5.05e-19

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 81.74  E-value: 5.05e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21387129    321 LTKEEAHEFRVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVPCVLLSFDDEQI 400
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQVIGKTI 80


                   ....
gi 21387129    401 LMWR 404
Cdd:smart01103  81 VLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 321-404 7.53e-17

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 75.51  E-value: 7.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21387129   321 LTKEEAHEFRVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVPCVLLSFDDEQI 400
Cdd:pfam01985   1 LTSKERRYLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKVLKNCREDRKEIAEELAEKTGAEVVQVIGRTI 80


                  ....
gi 21387129   401 LMWR 404
Cdd:pfam01985  81 VLYR 84
 
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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