NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|489080623|ref|WP_002990557|]
View 

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 2.61e-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: 168.40  E-value: 2.61e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623  12 VEQILDKANIAHQGL-------KLNALEGDFPDDLQPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSM 84
Cdd:cd00002    4 AIRLLDKAKIPYELHeyehdedASDGLEAAEKLGLDPEQVFKTLVVEGDKKGLVVAVVPVDEELDLKKLAKALGAKKVEM 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489080623  85 VPQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADL 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 2.61e-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: 168.40  E-value: 2.61e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623  12 VEQILDKANIAHQGL-------KLNALEGDFPDDLQPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSM 84
Cdd:cd00002    4 AIRLLDKAKIPYELHeyehdedASDGLEAAEKLGLDPEQVFKTLVVEGDKKGLVVAVVPVDEELDLKKLAKALGAKKVEM 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489080623  85 VPQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADL 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 4.58e-41

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: 134.67  E-value: 4.58e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623   12 VEQILDKANIAHQglkLNALEGDfPDDL-----------QPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNK 80
Cdd:TIGR00011   3 AIRLLDKAKIEYE---VHEYEVD-PDHLdgesaaeklgvDPHRVFKTLVAEGDKKGPVVAVIPGDEELDLKKLAKASGGK 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489080623   81 KVSMVPQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADL 155
Cdd:TIGR00011  79 KAEMADPKDAEKVTGYIRGGISPIG--QKKKFPTYIDESAKQLETIYVSGGKRGLQIELAPDDLIRLLDGTFADI 151
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 12-159 7.05e-34

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: 116.34  E-value: 7.05e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623  12 VEQILDKANIAHQglkLNALEGDFPDDLQ--------PSDIYKTLALTGDqTGPLIGIIPLTEHLSEKQLAKVSGNKKVS 83
Cdd:COG2606    3 VRRALDAAGIPYE---VVEHPEPAATAEEaaealgvpPEQIAKTLVFRGD-GGPVLAVVPGDRRLDLKKLAAALGAKKVE 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489080623  84 MVPQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADLKKRK 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 2.61e-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: 80.72  E-value: 2.61e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623   41 PSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSMVPQKDLQKTTGYIHGANNPVGIrQKHSYPIFIDQTA 120
Cdd:pfam04073  18 PGRIAKTLVLKDKKGKYVLVVVPGDREVDLKKLAKLLGVKRLRLASEEELLELTGVEPGGVTPFGL-KAKGVPVLVDESL 96

                          90       100
                  ....*....|....*....|....*..
gi 489080623  121 LEKGQIIVSAGEVGRSIKISSQALADF 147
Cdd:pfam04073  97 KDLPDVVVGAGENGATLRLSNADLRKL 123
PRK10670 PRK10670
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
39-159 1.09e-18

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


Pssm-ID: 182634  Cd Length: 159  Bit Score: 77.48  E-value: 1.09e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623  39 LQPSDIYKTL--ALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSMVPQKDLQKTTGYIHGANNPVGirQKHSYPIFI 116
Cdd:PRK10670  39 LNADQVYKTLlvAVNGDMKHLAVAVTPVAGQLDLKKVAKALGAKKVEMADPMVAQRSTGYLVGGISPLG--QKKRLPTVI 116

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 489080623 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 2.61e-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: 168.40  E-value: 2.61e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623  12 VEQILDKANIAHQGL-------KLNALEGDFPDDLQPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSM 84
Cdd:cd00002    4 AIRLLDKAKIPYELHeyehdedASDGLEAAEKLGLDPEQVFKTLVVEGDKKGLVVAVVPVDEELDLKKLAKALGAKKVEM 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489080623  85 VPQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADL 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 4.58e-41

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: 134.67  E-value: 4.58e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623   12 VEQILDKANIAHQglkLNALEGDfPDDL-----------QPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNK 80
Cdd:TIGR00011   3 AIRLLDKAKIEYE---VHEYEVD-PDHLdgesaaeklgvDPHRVFKTLVAEGDKKGPVVAVIPGDEELDLKKLAKASGGK 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489080623   81 KVSMVPQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADL 155
Cdd:TIGR00011  79 KAEMADPKDAEKVTGYIRGGISPIG--QKKKFPTYIDESAKQLETIYVSGGKRGLQIELAPDDLIRLLDGTFADI 151
EbsC COG2606
Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal ...
 12-159 7.05e-34

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: 116.34  E-value: 7.05e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623  12 VEQILDKANIAHQglkLNALEGDFPDDLQ--------PSDIYKTLALTGDqTGPLIGIIPLTEHLSEKQLAKVSGNKKVS 83
Cdd:COG2606    3 VRRALDAAGIPYE---VVEHPEPAATAEEaaealgvpPEQIAKTLVFRGD-GGPVLAVVPGDRRLDLKKLAAALGAKKVE 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489080623  84 MVPQKDLQKTTGYIHGANNPVGirQKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADLKKRK 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 7.96e-28

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: 100.31  E-value: 7.96e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623  38 DLQPSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSMVPQKDLQKTTGYIHGANNPVGirQKHSYPIFID 117
Cdd:cd04332   22 GVPPGQIAKTLVLKDDKGGLVLVVVPGDHELDLKKLAKALGAKKLRLASEEELEELTGCEPGGVGPFG--LKKGVPVVVD 99

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489080623 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 2.61e-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: 80.72  E-value: 2.61e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623   41 PSDIYKTLALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSMVPQKDLQKTTGYIHGANNPVGIrQKHSYPIFIDQTA 120
Cdd:pfam04073  18 PGRIAKTLVLKDKKGKYVLVVVPGDREVDLKKLAKLLGVKRLRLASEEELLELTGVEPGGVTPFGL-KAKGVPVLVDESL 96

                          90       100
                  ....*....|....*....|....*..
gi 489080623  121 LEKGQIIVSAGEVGRSIKISSQALADF 147
Cdd:pfam04073  97 KDLPDVVVGAGENGATLRLSNADLRKL 123
PRK10670 PRK10670
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
39-159 1.09e-18

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


Pssm-ID: 182634  Cd Length: 159  Bit Score: 77.48  E-value: 1.09e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080623  39 LQPSDIYKTL--ALTGDQTGPLIGIIPLTEHLSEKQLAKVSGNKKVSMVPQKDLQKTTGYIHGANNPVGirQKHSYPIFI 116
Cdd:PRK10670  39 LNADQVYKTLlvAVNGDMKHLAVAVTPVAGQLDLKKVAKALGAKKVEMADPMVAQRSTGYLVGGISPLG--QKKRLPTVI 116

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 489080623 117 DQTALEKGQIIVSAGEVGRSIKISSQALADFVGASFADLKKRK 159
Cdd:PRK10670 117 DAPAQEFATIYVSGGKRGLDIELAAGDLAKLLDAKFADIARRD 159
PA2301 cd04939
PA2301 is an uncharacterized Pseudomonas aeruginosa protein with a YbaK-like domain of unknown ...
 78-150 6.86e-03

PA2301 is an uncharacterized Pseudomonas aeruginosa protein with a YbaK-like domain of unknown function. The YbaK-like domain family includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, and ProX. 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 a single-domain INS homolog such as YbaK, ProX, or PrdX which supplies the function of INS in trans.


Pssm-ID: 240137  Cd Length: 139  Bit Score: 35.01  E-value: 6.86e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489080623  78 GNKKVSMVPQKDLQKTTGYIHGANNPVGIrqKHSYPIFIDQTALEKGQIIVSAGEVGRSIKISSQALADFVGA 150
Cdd:cd04939   66 GARKASFAPMETAVELTGMEYGGITPVGL--PAGWPILVDSAVAERPAVVIGSGVRRSKLLLPGAALAELPGA 136
 
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