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Conserved domains on  [gi|500586394|ref|WP_011953438|]
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D-aminoacyl-tRNA deacylase [Limosilactobacillus reuteri]

Protein Classification

D-aminoacyl-tRNA deacylase( domain architecture ID 10003927)

D-aminoacyl-tRNA deacylase hydrolyzes D-aminoacyl-tRNA into D-amino acids and free tRNA which may be a defense mechanism against harmful effects of incorporating D-amino acids

CATH:  3.50.80.10
EC:  3.1.1.96
Gene Ontology:  GO:0000049|GO:0002161|GO:0006399|GO:0051499
PubMed:  35662005
SCOP:  4003261

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Dtd COG1490
D-aminoacyl-tRNA deacylase [Translation, ribosomal structure and biogenesis];
1-144 6.61e-92

D-aminoacyl-tRNA deacylase [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 441099  Cd Length: 147  Bit Score: 262.62  E-value: 6.61e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394   1 MRVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKMNKGLRDVNGAILSVSQFT 80
Cdd:COG1490    1 MRAVIQRVSEASVTVDGEVVGEIGKGLLVLLGVEKGDTEEDADWLARKILNLRIFEDENGKMNLSLLDVGGELLVVSQFT 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500586394  81 LYADTKHGNRPGFSQAASPEIAEPLYDLFNQKLAATGIPVETGHFGAMMKIDLENDGPTTIIYE 144
Cdd:COG1490   81 LYADTRKGRRPSFSKAAPPEEAEPLYEYFVEALRELGLPVETGVFGADMQVSLVNDGPVTILLD 144
 
Name Accession Description Interval E-value
Dtd COG1490
D-aminoacyl-tRNA deacylase [Translation, ribosomal structure and biogenesis];
1-144 6.61e-92

D-aminoacyl-tRNA deacylase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441099  Cd Length: 147  Bit Score: 262.62  E-value: 6.61e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394   1 MRVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKMNKGLRDVNGAILSVSQFT 80
Cdd:COG1490    1 MRAVIQRVSEASVTVDGEVVGEIGKGLLVLLGVEKGDTEEDADWLARKILNLRIFEDENGKMNLSLLDVGGELLVVSQFT 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500586394  81 LYADTKHGNRPGFSQAASPEIAEPLYDLFNQKLAATGIPVETGHFGAMMKIDLENDGPTTIIYE 144
Cdd:COG1490   81 LYADTRKGRRPSFSKAAPPEEAEPLYEYFVEALRELGLPVETGVFGADMQVSLVNDGPVTILLD 144
Tyr_Deacylase pfam02580
D-Tyr-tRNA(Tyr) deacylase; This family comprises of several D-Tyr-tRNA(Tyr) deacylase proteins. ...
 2-144 1.80e-84

D-Tyr-tRNA(Tyr) deacylase; This family comprises of several D-Tyr-tRNA(Tyr) deacylase proteins. Cell growth inhibition by several d-amino acids can be explained by an in vivo production of d-aminoacyl-tRNA molecules. Escherichia coli and yeast cells express an enzyme, d-Tyr-tRNA(Tyr) deacylase, capable of recycling such d-aminoacyl-tRNA molecules into free tRNA and d-amino acid. Accordingly, upon inactivation of the genes of the above deacylases, the toxicity of d-amino acids increases. Orthologues of the deacylase are found in many cells.The D-aminoacyl-tRNA deacylase (DTD) enzyme is homodimeric with two active sites located at the dimeric interface. Each active site carries an invariant Gly-cisPro dipeptide motif in each monomer. The interaction between the dipeptide motifs from each monomer ensures substrate stereospecificity. This family also includes a subclass of DTDs which is present in Chordata and harbors a Gly-transPro motif. The cis to trans switch is the key to Animal DTDs (ATD) gaining of L-chiral selectivity. This 'gain of function' through relaxation of substrate chiral specificity underlies ATD's capability of correcting the error in tRNA selection.


Pssm-ID: 460603  Cd Length: 144  Bit Score: 243.81  E-value: 1.80e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394    2 RVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKMNKGLRDVNGAILSVSQFTL 81
Cdd:pfam02580   1 RAVIQRVSSASVTVDGEVVGSIGRGLLVLVGVGKGDTEEDADKLAKKILNLRIFEDENGKMNLSLKDVGGEILVVSQFTL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500586394   82 YADTKHGNRPGFSQAASPEIAEPLYDLFNQKL-AATGIPVETGHFGAMMKIDLENDGPTTIIYE 144
Cdd:pfam02580  81 YADTRKGRRPSFHAAAPPEEAEPLYERFVEKLrKEYGEKVETGVFGADMQVSLVNDGPVTILLD 144
Dtyr_deacylase cd00563
D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of ...
 1-144 1.19e-76

D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not in archea; beta barrel-like fold structure; forms homodimers in which two surface cavities serve as the active site for tRNA binding


Pssm-ID: 238316  Cd Length: 145  Bit Score: 224.08  E-value: 1.19e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394   1 MRVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKMNKGLRDVNGAILSVSQFT 80
Cdd:cd00563    1 MRAVIQRVSEASVTVDGEVVGAIGQGLLVLVGVTHDDTEEDAEYLARKILNLRIFEDEEGKMNLSVKDVNGEILVVSQFT 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500586394  81 LYADTKHGNRPGFSQAASPEIAEPLYDLFNQKLAATGIPVETGHFGAMMKIDLENDGPTTIIYE 144
Cdd:cd00563   81 LYADTKKGRRPSFSAAAPPDKAEPLYESFVELLREKGIKVETGVFGAMMQVSLVNDGPVTIILD 144
TIGR00256 TIGR00256
D-tyrosyl-tRNA(Tyr) deacylase; This homodimeric enzyme appears able to cleave any D-amino acid ...
 1-142 2.11e-63

D-tyrosyl-tRNA(Tyr) deacylase; This homodimeric enzyme appears able to cleave any D-amino acid (and glycine, which does not have distinct D/L forms) from charged tRNA. The name reflects characterization with respect to D-Tyr on tRNA(Tyr) as established in the literature, but substrate specificity seems much broader. [Protein synthesis, tRNA aminoacylation]


Pssm-ID: 129358  Cd Length: 145  Bit Score: 190.45  E-value: 2.11e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394    1 MRVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKMNKGLRDVNGAILSVSQFT 80
Cdd:TIGR00256   1 MIALIQRVSQASVTVEGEVIGEIGAGLLVLLGVEKDDDEQKADKLAEKVLNYRIFSDSEGKMNLNVQQAGGEILSVSQFT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 500586394   81 LYADTKHGNRPGFSQAASPEIAEPLYDLFNQKLAATGIPVETGHFGAMMKIDLENDGPTTII 142
Cdd:TIGR00256  81 LAADTKKGMRPSFSKGASPDRAEELYEYFVELCREKGMKVQTGRFAADMQVSLTNDGPVTFW 142
PTZ00120 PTZ00120
D-tyrosyl-tRNA(Tyr) deacylase; Provisional
 1-142 1.59e-52

D-tyrosyl-tRNA(Tyr) deacylase; Provisional


Pssm-ID: 185458  Cd Length: 154  Bit Score: 163.25  E-value: 1.59e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394   1 MRVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKM-NKGLRDVNGAILSVSQF 79
Cdd:PTZ00120   1 MRVVIQRVLSASVTVEGEVVGSIGKGLVLLVGIHEEDTWEDADYIIRKCLKLRLWPDEGGKMwDRSVKDKDYEVLVVSQF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500586394  80 TLYAdTKHGNRPGFSQAASPEIAEPLYDLFNQKLAATGIP--VETGHFGAMMKIDLENDGPTTII 142
Cdd:PTZ00120  81 TLFN-VKKGNKPDFHLAMSPEDALPLYNKFVEKFKKEYAPekIKTGKFGQYMNVSLVNDGPVTII 144
 
Name Accession Description Interval E-value
Dtd COG1490
D-aminoacyl-tRNA deacylase [Translation, ribosomal structure and biogenesis];
1-144 6.61e-92

D-aminoacyl-tRNA deacylase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441099  Cd Length: 147  Bit Score: 262.62  E-value: 6.61e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394   1 MRVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKMNKGLRDVNGAILSVSQFT 80
Cdd:COG1490    1 MRAVIQRVSEASVTVDGEVVGEIGKGLLVLLGVEKGDTEEDADWLARKILNLRIFEDENGKMNLSLLDVGGELLVVSQFT 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500586394  81 LYADTKHGNRPGFSQAASPEIAEPLYDLFNQKLAATGIPVETGHFGAMMKIDLENDGPTTIIYE 144
Cdd:COG1490   81 LYADTRKGRRPSFSKAAPPEEAEPLYEYFVEALRELGLPVETGVFGADMQVSLVNDGPVTILLD 144
Tyr_Deacylase pfam02580
D-Tyr-tRNA(Tyr) deacylase; This family comprises of several D-Tyr-tRNA(Tyr) deacylase proteins. ...
 2-144 1.80e-84

D-Tyr-tRNA(Tyr) deacylase; This family comprises of several D-Tyr-tRNA(Tyr) deacylase proteins. Cell growth inhibition by several d-amino acids can be explained by an in vivo production of d-aminoacyl-tRNA molecules. Escherichia coli and yeast cells express an enzyme, d-Tyr-tRNA(Tyr) deacylase, capable of recycling such d-aminoacyl-tRNA molecules into free tRNA and d-amino acid. Accordingly, upon inactivation of the genes of the above deacylases, the toxicity of d-amino acids increases. Orthologues of the deacylase are found in many cells.The D-aminoacyl-tRNA deacylase (DTD) enzyme is homodimeric with two active sites located at the dimeric interface. Each active site carries an invariant Gly-cisPro dipeptide motif in each monomer. The interaction between the dipeptide motifs from each monomer ensures substrate stereospecificity. This family also includes a subclass of DTDs which is present in Chordata and harbors a Gly-transPro motif. The cis to trans switch is the key to Animal DTDs (ATD) gaining of L-chiral selectivity. This 'gain of function' through relaxation of substrate chiral specificity underlies ATD's capability of correcting the error in tRNA selection.


Pssm-ID: 460603  Cd Length: 144  Bit Score: 243.81  E-value: 1.80e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394    2 RVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKMNKGLRDVNGAILSVSQFTL 81
Cdd:pfam02580   1 RAVIQRVSSASVTVDGEVVGSIGRGLLVLVGVGKGDTEEDADKLAKKILNLRIFEDENGKMNLSLKDVGGEILVVSQFTL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500586394   82 YADTKHGNRPGFSQAASPEIAEPLYDLFNQKL-AATGIPVETGHFGAMMKIDLENDGPTTIIYE 144
Cdd:pfam02580  81 YADTRKGRRPSFHAAAPPEEAEPLYERFVEKLrKEYGEKVETGVFGADMQVSLVNDGPVTILLD 144
Dtyr_deacylase cd00563
D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of ...
 1-144 1.19e-76

D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not in archea; beta barrel-like fold structure; forms homodimers in which two surface cavities serve as the active site for tRNA binding


Pssm-ID: 238316  Cd Length: 145  Bit Score: 224.08  E-value: 1.19e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394   1 MRVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKMNKGLRDVNGAILSVSQFT 80
Cdd:cd00563    1 MRAVIQRVSEASVTVDGEVVGAIGQGLLVLVGVTHDDTEEDAEYLARKILNLRIFEDEEGKMNLSVKDVNGEILVVSQFT 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500586394  81 LYADTKHGNRPGFSQAASPEIAEPLYDLFNQKLAATGIPVETGHFGAMMKIDLENDGPTTIIYE 144
Cdd:cd00563   81 LYADTKKGRRPSFSAAAPPDKAEPLYESFVELLREKGIKVETGVFGAMMQVSLVNDGPVTIILD 144
TIGR00256 TIGR00256
D-tyrosyl-tRNA(Tyr) deacylase; This homodimeric enzyme appears able to cleave any D-amino acid ...
 1-142 2.11e-63

D-tyrosyl-tRNA(Tyr) deacylase; This homodimeric enzyme appears able to cleave any D-amino acid (and glycine, which does not have distinct D/L forms) from charged tRNA. The name reflects characterization with respect to D-Tyr on tRNA(Tyr) as established in the literature, but substrate specificity seems much broader. [Protein synthesis, tRNA aminoacylation]


Pssm-ID: 129358  Cd Length: 145  Bit Score: 190.45  E-value: 2.11e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394    1 MRVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKMNKGLRDVNGAILSVSQFT 80
Cdd:TIGR00256   1 MIALIQRVSQASVTVEGEVIGEIGAGLLVLLGVEKDDDEQKADKLAEKVLNYRIFSDSEGKMNLNVQQAGGEILSVSQFT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 500586394   81 LYADTKHGNRPGFSQAASPEIAEPLYDLFNQKLAATGIPVETGHFGAMMKIDLENDGPTTII 142
Cdd:TIGR00256  81 LAADTKKGMRPSFSKGASPDRAEELYEYFVELCREKGMKVQTGRFAADMQVSLTNDGPVTFW 142
PTZ00120 PTZ00120
D-tyrosyl-tRNA(Tyr) deacylase; Provisional
 1-142 1.59e-52

D-tyrosyl-tRNA(Tyr) deacylase; Provisional


Pssm-ID: 185458  Cd Length: 154  Bit Score: 163.25  E-value: 1.59e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500586394   1 MRVVLQKVNHAAVSIDDEVVGKIGLGYFLLVGFAPDDTEEKLNYLVHKITNLRVFEDENGKM-NKGLRDVNGAILSVSQF 79
Cdd:PTZ00120   1 MRVVIQRVLSASVTVEGEVVGSIGKGLVLLVGIHEEDTWEDADYIIRKCLKLRLWPDEGGKMwDRSVKDKDYEVLVVSQF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500586394  80 TLYAdTKHGNRPGFSQAASPEIAEPLYDLFNQKLAATGIP--VETGHFGAMMKIDLENDGPTTII 142
Cdd:PTZ00120  81 TLFN-VKKGNKPDFHLAMSPEDALPLYNKFVEKFKKEYAPekIKTGKFGQYMNVSLVNDGPVTII 144
 
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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