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Conserved domains on  [gi|1622294787|ref|WP_136262541|]
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aminoacyl-tRNA deacylase [Streptococcus pyogenes]

Protein Classification

aminoacyl-tRNA deacylase( domain architecture ID 10025411)

aminoacyl-tRNA deacylase of the YbaK/EbsC family

Gene Ontology:  GO:0016829

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbaK_deacylase cd00002
This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia ...
 12-155 5.79e-54

This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS) inserted (INS) editing domain. The bacterial amino acid trans-editing enzyme YbaK is a deacylase that hydrolyzes cysteinyl-tRNA(Pro)'s mischarged by prolyl-tRNA synthetase. YbaK also hydrolyzes glycyl-tRNA's, alanyl-tRNA's, seryl-tRNA's, and prolyl-tRNA's. YbaK is homologous to the INS domain of prolyl-tRNA synthetase (ProRS) as well as the trans-editing enzyme ProX of Aeropyrum pernix which hydrolyzes alanyl-tRNA's and glycyl-tRNA's.


:

Pssm-ID: 237976 [Multi-domain]  Cd Length: 152  Bit Score: 167.24  E-value: 5.79e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  12 VEQILDKANIAHQGL-------KLNALEGDFPDDLQPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSM 84
Cdd:cd00002     4 AIRLLDKAKIPYELHeyehdedASDGLEAAEKLGLDPEQVFKTLVVEGDKKGLVVAVVPVDEELDLKKLAKALGAKKVEM 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622294787  85 VHQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADL 155
Cdd:cd00002    84 APPKDAERLTGYIRGGISPLG--QKKRLPTVIDESALDLDTIYVSAGKRGLQIELAPQDLAKLTGAKFADI 152
 
Name Accession Description Interval E-value
YbaK_deacylase cd00002
This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia ...
 12-155 5.79e-54

This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS) inserted (INS) editing domain. The bacterial amino acid trans-editing enzyme YbaK is a deacylase that hydrolyzes cysteinyl-tRNA(Pro)'s mischarged by prolyl-tRNA synthetase. YbaK also hydrolyzes glycyl-tRNA's, alanyl-tRNA's, seryl-tRNA's, and prolyl-tRNA's. YbaK is homologous to the INS domain of prolyl-tRNA synthetase (ProRS) as well as the trans-editing enzyme ProX of Aeropyrum pernix which hydrolyzes alanyl-tRNA's and glycyl-tRNA's.


Pssm-ID: 237976 [Multi-domain]  Cd Length: 152  Bit Score: 167.24  E-value: 5.79e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  12 VEQILDKANIAHQGL-------KLNALEGDFPDDLQPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSM 84
Cdd:cd00002     4 AIRLLDKAKIPYELHeyehdedASDGLEAAEKLGLDPEQVFKTLVVEGDKKGLVVAVVPVDEELDLKKLAKALGAKKVEM 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622294787  85 VHQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADL 155
Cdd:cd00002    84 APPKDAERLTGYIRGGISPLG--QKKRLPTVIDESALDLDTIYVSAGKRGLQIELAPQDLAKLTGAKFADI 152
YbaK_EbsC TIGR00011
Cys-tRNA(Pro) deacylase; This model represents the YbaK family, bacterial proteins whose full ...
 12-155 2.06e-40

Cys-tRNA(Pro) deacylase; This model represents the YbaK family, bacterial proteins whose full length sequence is homologous to an insertion domain in proline--tRNA ligases. The domain deacylates mischarged tRNAs. The YbaK protein of Haemophilus influenzae (HI1434) likewise deacylates Ala-tRNA(Pro), but not the correctly charged Pro-tRNA(Pro). A crystallographic study of HI1434 suggests a nucleotide binding function. Previously, a member of this family was described as EbsC and was thought to be involved in cell wall metabolism. [Protein synthesis, tRNA aminoacylation]


Pssm-ID: 272853 [Multi-domain]  Cd Length: 152  Bit Score: 133.13  E-value: 2.06e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  12 VEQILDKANIAHQglkLNALEGDfPDDL-----------QPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNK 80
Cdd:TIGR00011   3 AIRLLDKAKIEYE---VHEYEVD-PDHLdgesaaeklgvDPHRVFKTLVAEGDKKGPVVAVIPGDEELDLKKLAKASGGK 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622294787  81 KVSMVHQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADL 155
Cdd:TIGR00011  79 KAEMADPKDAEKVTGYIRGGISPIG--QKKKFPTYIDESAKQLETIYVSGGKRGLQIELAPDDLIRLLDGTFADI 151
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 12-159 1.49e-33

Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442018 [Multi-domain]  Cd Length: 152  Bit Score: 115.57  E-value: 1.49e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  12 VEQILDKANIAHQglkLNALEGDFPDDLQ--------PSDIYKTLALTGDqTGPLIGIIPLTEHLSEKQLAKVSGNKKVS 83
Cdd:COG2606     3 VRRALDAAGIPYE---VVEHPEPAATAEEaaealgvpPEQIAKTLVFRGD-GGPVLAVVPGDRRLDLKKLAAALGAKKVE 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622294787  84 MVHQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADLKKRK 159
Cdd:COG2606    79 MADPEEVERLTGYEVGGVSPFG--LKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGATVADIARPA 152
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 41-147 1.44e-20

Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with the tRNA synthetase class II core domain (pfam00587). It is involved in the tRNA editing of mis-charged tRNAs including Cys-tRNA(Pro), Cys-tRNA(Cys), Ala-tRNA(Pro). The structure of this domain shows a novel fold.


Pssm-ID: 427693 [Multi-domain]  Cd Length: 123  Bit Score: 81.49  E-value: 1.44e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  41 PSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSMVHQKDLQKTTGYIHGANNPVGIrQKHSYPIFIDQTA 120
Cdd:pfam04073  18 PGRIAKTLVLKDKKGKYVLVVVPGDREVDLKKLAKLLGVKRLRLASEEELLELTGVEPGGVTPFGL-KAKGVPVLVDESL 96

                          90       100
                  ....*....|....*....|....*..
gi 1622294787 121 LEKGQIIVSAGEVGRSIKISSQALADF 147
Cdd:pfam04073  97 KDLPDVVVGAGENGATLRLSNADLRKL 123
PRK10670 PRK10670
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
39-159 8.81e-19

Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;


Pssm-ID: 182634  Cd Length: 159  Bit Score: 77.86  E-value: 8.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  39 LQPSDIYKTL--ALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSMVHQKDLQKTTGYIHGANNPVGirQKHSYPIFI 116
Cdd:PRK10670   39 LNADQVYKTLlvAVNGDMKHLAVAVTPVAGQLDLKKVAKALGAKKVEMADPMVAQRSTGYLVGGISPLG--QKKRLPTVI 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1622294787 117 DQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADLKKRK 159
Cdd:PRK10670  117 DAPAQEFATIYVSGGKRGLDIELAAGDLAKLLDAKFADIARRD 159
 
Name Accession Description Interval E-value
YbaK_deacylase cd00002
This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia ...
 12-155 5.79e-54

This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS) inserted (INS) editing domain. The bacterial amino acid trans-editing enzyme YbaK is a deacylase that hydrolyzes cysteinyl-tRNA(Pro)'s mischarged by prolyl-tRNA synthetase. YbaK also hydrolyzes glycyl-tRNA's, alanyl-tRNA's, seryl-tRNA's, and prolyl-tRNA's. YbaK is homologous to the INS domain of prolyl-tRNA synthetase (ProRS) as well as the trans-editing enzyme ProX of Aeropyrum pernix which hydrolyzes alanyl-tRNA's and glycyl-tRNA's.


Pssm-ID: 237976 [Multi-domain]  Cd Length: 152  Bit Score: 167.24  E-value: 5.79e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  12 VEQILDKANIAHQGL-------KLNALEGDFPDDLQPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSM 84
Cdd:cd00002     4 AIRLLDKAKIPYELHeyehdedASDGLEAAEKLGLDPEQVFKTLVVEGDKKGLVVAVVPVDEELDLKKLAKALGAKKVEM 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622294787  85 VHQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADL 155
Cdd:cd00002    84 APPKDAERLTGYIRGGISPLG--QKKRLPTVIDESALDLDTIYVSAGKRGLQIELAPQDLAKLTGAKFADI 152
YbaK_EbsC TIGR00011
Cys-tRNA(Pro) deacylase; This model represents the YbaK family, bacterial proteins whose full ...
 12-155 2.06e-40

Cys-tRNA(Pro) deacylase; This model represents the YbaK family, bacterial proteins whose full length sequence is homologous to an insertion domain in proline--tRNA ligases. The domain deacylates mischarged tRNAs. The YbaK protein of Haemophilus influenzae (HI1434) likewise deacylates Ala-tRNA(Pro), but not the correctly charged Pro-tRNA(Pro). A crystallographic study of HI1434 suggests a nucleotide binding function. Previously, a member of this family was described as EbsC and was thought to be involved in cell wall metabolism. [Protein synthesis, tRNA aminoacylation]


Pssm-ID: 272853 [Multi-domain]  Cd Length: 152  Bit Score: 133.13  E-value: 2.06e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  12 VEQILDKANIAHQglkLNALEGDfPDDL-----------QPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNK 80
Cdd:TIGR00011   3 AIRLLDKAKIEYE---VHEYEVD-PDHLdgesaaeklgvDPHRVFKTLVAEGDKKGPVVAVIPGDEELDLKKLAKASGGK 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622294787  81 KVSMVHQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADL 155
Cdd:TIGR00011  79 KAEMADPKDAEKVTGYIRGGISPIG--QKKKFPTYIDESAKQLETIYVSGGKRGLQIELAPDDLIRLLDGTFADI 151
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 12-159 1.49e-33

Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442018 [Multi-domain]  Cd Length: 152  Bit Score: 115.57  E-value: 1.49e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  12 VEQILDKANIAHQglkLNALEGDFPDDLQ--------PSDIYKTLALTGDqTGPLIGIIPLTEHLSEKQLAKVSGNKKVS 83
Cdd:COG2606     3 VRRALDAAGIPYE---VVEHPEPAATAEEaaealgvpPEQIAKTLVFRGD-GGPVLAVVPGDRRLDLKKLAAALGAKKVE 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622294787  84 MVHQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADLKKRK 159
Cdd:COG2606    79 MADPEEVERLTGYEVGGVSPFG--LKKGLPVYVDESLLEFDEVYVSAGDRGLLVELAPADLARLTGATVADIARPA 152
YbaK_like cd04332
YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of ...
 38-150 2.89e-27

YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation. Organisms whose ProRS lacks the INS domain express an INS homolog in trans (e.g. YbaK, ProX, or PrdX).


Pssm-ID: 239824 [Multi-domain]  Cd Length: 136  Bit Score: 99.15  E-value: 2.89e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  38 DLQPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSMVHQKDLQKTTGYIHGANNPVGirQKHSYPIFID 117
Cdd:cd04332    22 GVPPGQIAKTLVLKDDKGGLVLVVVPGDHELDLKKLAKALGAKKLRLASEEELEELTGCEPGGVGPFG--LKKGVPVVVD 99

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1622294787 118 QTALEKGQIIVSAGEVGRSIKISSQALADFVGA 150
Cdd:cd04332   100 ESLLELEDVYVGAGERGADLHLSPADLLRLLGE 132
tRNA_edit pfam04073
Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with ...
 41-147 1.44e-20

Aminoacyl-tRNA editing domain; This domain is found either on its own or in association with the tRNA synthetase class II core domain (pfam00587). It is involved in the tRNA editing of mis-charged tRNAs including Cys-tRNA(Pro), Cys-tRNA(Cys), Ala-tRNA(Pro). The structure of this domain shows a novel fold.


Pssm-ID: 427693 [Multi-domain]  Cd Length: 123  Bit Score: 81.49  E-value: 1.44e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  41 PSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSMVHQKDLQKTTGYIHGANNPVGIrQKHSYPIFIDQTA 120
Cdd:pfam04073  18 PGRIAKTLVLKDKKGKYVLVVVPGDREVDLKKLAKLLGVKRLRLASEEELLELTGVEPGGVTPFGL-KAKGVPVLVDESL 96

                          90       100
                  ....*....|....*....|....*..
gi 1622294787 121 LEKGQIIVSAGEVGRSIKISSQALADF 147
Cdd:pfam04073  97 KDLPDVVVGAGENGATLRLSNADLRKL 123
PRK10670 PRK10670
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
39-159 8.81e-19

Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;


Pssm-ID: 182634  Cd Length: 159  Bit Score: 77.86  E-value: 8.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622294787  39 LQPSDIYKTL--ALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSMVHQKDLQKTTGYIHGANNPVGirQKHSYPIFI 116
Cdd:PRK10670   39 LNADQVYKTLlvAVNGDMKHLAVAVTPVAGQLDLKKVAKALGAKKVEMADPMVAQRSTGYLVGGISPLG--QKKRLPTVI 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1622294787 117 DQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADLKKRK 159
Cdd:PRK10670  117 DAPAQEFATIYVSGGKRGLDIELAAGDLAKLLDAKFADIARRD 159
 
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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