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Conserved domains on  [gi|1938900672]
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Chain c, MRPL39

Protein Classification

threonine--tRNA ligase family protein( domain architecture ID 1000183)

threonine--tRNA ligase family protein such as threonine--tRNA ligase ThrRS, also termed cytoplasmic threonine--tRNA ligase, a class II aminoacyl-tRNA synthetase (aaRS) that plays an essential role in protein synthesis by catalyzing the aminoacylation of tRNA(Thr), generating aminoacyl-tRNA, and editing misacylation, and such as the large ribosomal subunit protein mL39.

Gene Ontology:  GO:0000166

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN02908 super family cl31949
threonyl-tRNA synthetase
 40-266 3.11e-26

threonyl-tRNA synthetase


The actual alignment was detected with superfamily member PLN02908:

Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 108.32  E-value: 3.11e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672  40 GTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFLTFKDDDPGEVnkaYWRSCAMMMGCVIE 119
Cdd:PLN02908   59 GAVKDGKKWVTTPMDIAKEISKGLANSALIAQVDGVLWDMTRPLEGDCKLKLFKFDDDEGRDT---FWHSSAHILGEALE 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672 120 RafkdEYVVSLVRAPEVPVIAGaFCYDVVLDKR-LDEwmptkENLHSFTKDARALIYKDLPFETLEVEAKVALEIFQHNK 198
Cdd:PLN02908  136 L----EYGCKLCIGPCTTRGEG-FYYDAFYGDRtLNE-----EDFKPIEARAEKAVKEKQPFERIEVTREEALEMFSENK 205

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1938900672 199 YKLDFIEEKasqnPE-RIVKLHRFGDFIDVSEGPLIPRTSI-----CFQYEVSAVHNLQTQSSLVRRFqGLSLP 266
Cdd:PLN02908  206 FKVEIINDL----PEdATITVYRCGPLVDLCRGPHIPNTSFvkafaCLKASSAYWRGDVDRESLQRVY-GISFP 274
 
Name Accession Description Interval E-value
PLN02908 PLN02908
threonyl-tRNA synthetase
 40-266 3.11e-26

threonyl-tRNA synthetase


Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 108.32  E-value: 3.11e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672  40 GTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFLTFKDDDPGEVnkaYWRSCAMMMGCVIE 119
Cdd:PLN02908   59 GAVKDGKKWVTTPMDIAKEISKGLANSALIAQVDGVLWDMTRPLEGDCKLKLFKFDDDEGRDT---FWHSSAHILGEALE 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672 120 RafkdEYVVSLVRAPEVPVIAGaFCYDVVLDKR-LDEwmptkENLHSFTKDARALIYKDLPFETLEVEAKVALEIFQHNK 198
Cdd:PLN02908  136 L----EYGCKLCIGPCTTRGEG-FYYDAFYGDRtLNE-----EDFKPIEARAEKAVKEKQPFERIEVTREEALEMFSENK 205

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1938900672 199 YKLDFIEEKasqnPE-RIVKLHRFGDFIDVSEGPLIPRTSI-----CFQYEVSAVHNLQTQSSLVRRFqGLSLP 266
Cdd:PLN02908  206 FKVEIINDL----PEdATITVYRCGPLVDLCRGPHIPNTSFvkafaCLKASSAYWRGDVDRESLQRVY-GISFP 274
TGS cd01616
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; ...
 33-92 9.65e-23

TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; This family includes eukaryotic and some bacterial threonyl-tRNA synthetases (ThrRSs), a distinct Obg family GTPases, and guanosine polyphosphate hydrolase (SpoT) and synthetase (RelA), which are involved in stringent response in bacteria, as well as uridine kinase (UDK) from Thermotogales. All family members contain a TGS domain named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. It is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. The functions of the TGS domain remains unclear, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, with a regulatory role.


Pssm-ID: 340455 [Multi-domain]  Cd Length: 61  Bit Score: 88.82  E-value: 9.65e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672  33 HVGKTdPGTVFVMNKnISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFL 92
Cdd:cd01616     4 TVGKT-PGTVFVMNK-GATAYSCAMHLHEDYCRKSILALVDGQLWDMYYPLTKGDEIKFL 61
ThrS COG0441
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA ...
 65-239 1.48e-19

Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases


Pssm-ID: 440210 [Multi-domain]  Cd Length: 639  Bit Score: 88.55  E-value: 1.48e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672  65 RKSILALVDGQPWDMYKPLTKSCEIKFLTFKDDDPGEVnkaYWRSCAMMMGCVIERAFkdeyvvslvraPEV-----PVI 139
Cdd:COG0441    33 KAAVAAKVNGELVDLSTPIEEDAELEIVTFDDEEGLEI---LRHSAAHLLAQAVKRLY-----------PDAkltigPVI 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672 140 AGAFCYDVVLDKRLdewmpTKENLHSFTKDARALIYKDLPFETLEVEAKVALEIFQ--HNKYKLDFIEEKASqnpERIVK 217
Cdd:COG0441    99 ENGFYYDFDLERPF-----TPEDLEKIEKEMKEIIKEDLPIEREEVSREEAIELFKekGEPYKVELIEDIPE---DEEIS 170

                         170       180
                  ....*....|....*....|..
gi 1938900672 218 LHRFGDFIDVSEGPLIPRTSIC 239
Cdd:COG0441   171 LYRQGEFVDLCRGPHVPSTGKI 192
TGS pfam02824
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain ...
 50-93 4.29e-03

TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organizm, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.


Pssm-ID: 427005 [Multi-domain]  Cd Length: 60  Bit Score: 34.83  E-value: 4.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1938900672  50 STPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFLT 93
Cdd:pfam02824  17 ATPEDFAYAIHTSLAKKFIYAKVNGQLVGLDHPLEDGDVVEIVT 60
 
Name Accession Description Interval E-value
PLN02908 PLN02908
threonyl-tRNA synthetase
 40-266 3.11e-26

threonyl-tRNA synthetase


Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 108.32  E-value: 3.11e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672  40 GTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFLTFKDDDPGEVnkaYWRSCAMMMGCVIE 119
Cdd:PLN02908   59 GAVKDGKKWVTTPMDIAKEISKGLANSALIAQVDGVLWDMTRPLEGDCKLKLFKFDDDEGRDT---FWHSSAHILGEALE 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672 120 RafkdEYVVSLVRAPEVPVIAGaFCYDVVLDKR-LDEwmptkENLHSFTKDARALIYKDLPFETLEVEAKVALEIFQHNK 198
Cdd:PLN02908  136 L----EYGCKLCIGPCTTRGEG-FYYDAFYGDRtLNE-----EDFKPIEARAEKAVKEKQPFERIEVTREEALEMFSENK 205

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1938900672 199 YKLDFIEEKasqnPE-RIVKLHRFGDFIDVSEGPLIPRTSI-----CFQYEVSAVHNLQTQSSLVRRFqGLSLP 266
Cdd:PLN02908  206 FKVEIINDL----PEdATITVYRCGPLVDLCRGPHIPNTSFvkafaCLKASSAYWRGDVDRESLQRVY-GISFP 274
TGS cd01616
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; ...
 33-92 9.65e-23

TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; This family includes eukaryotic and some bacterial threonyl-tRNA synthetases (ThrRSs), a distinct Obg family GTPases, and guanosine polyphosphate hydrolase (SpoT) and synthetase (RelA), which are involved in stringent response in bacteria, as well as uridine kinase (UDK) from Thermotogales. All family members contain a TGS domain named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. It is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. The functions of the TGS domain remains unclear, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, with a regulatory role.


Pssm-ID: 340455 [Multi-domain]  Cd Length: 61  Bit Score: 88.82  E-value: 9.65e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672  33 HVGKTdPGTVFVMNKnISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFL 92
Cdd:cd01616     4 TVGKT-PGTVFVMNK-GATAYSCAMHLHEDYCRKSILALVDGQLWDMYYPLTKGDEIKFL 61
TGS_ThrRS cd01667
TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar ...
 40-98 4.33e-20

TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar proteins; ThrRS, also termed cytoplasmic threonine--tRNA ligase, is a class II aminoacyl-tRNA synthetase (aaRS) that plays an essential role in protein synthesis by catalyzing the aminoacylation of tRNA(Thr), generating aminoacyl-tRNA, and editing misacylation. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. TGS is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340458 [Multi-domain]  Cd Length: 65  Bit Score: 82.15  E-value: 4.33e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1938900672  40 GTVFVMNKNIsTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFLTFKDDD 98
Cdd:cd01667     8 GSVKEFPKGT-TPLDIAKSISPGLAKKAVAAKVNGELVDLSRPLEEDAELEILTFDDPE 65
ThrS COG0441
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA ...
 65-239 1.48e-19

Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases


Pssm-ID: 440210 [Multi-domain]  Cd Length: 639  Bit Score: 88.55  E-value: 1.48e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672  65 RKSILALVDGQPWDMYKPLTKSCEIKFLTFKDDDPGEVnkaYWRSCAMMMGCVIERAFkdeyvvslvraPEV-----PVI 139
Cdd:COG0441    33 KAAVAAKVNGELVDLSTPIEEDAELEIVTFDDEEGLEI---LRHSAAHLLAQAVKRLY-----------PDAkltigPVI 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672 140 AGAFCYDVVLDKRLdewmpTKENLHSFTKDARALIYKDLPFETLEVEAKVALEIFQ--HNKYKLDFIEEKASqnpERIVK 217
Cdd:COG0441    99 ENGFYYDFDLERPF-----TPEDLEKIEKEMKEIIKEDLPIEREEVSREEAIELFKekGEPYKVELIEDIPE---DEEIS 170

                         170       180
                  ....*....|....*....|..
gi 1938900672 218 LHRFGDFIDVSEGPLIPRTSIC 239
Cdd:COG0441   171 LYRQGEFVDLCRGPHVPSTGKI 192
PRK12444 PRK12444
threonyl-tRNA synthetase; Reviewed
 65-236 2.98e-11

threonyl-tRNA synthetase; Reviewed


Pssm-ID: 183530 [Multi-domain]  Cd Length: 639  Bit Score: 64.00  E-value: 2.98e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672  65 RKSILALVDGQPWDMYKPLTKSCEIKFLTFKDDDPGEVnkaYWRSCAMMMGCVIERAFKDeyvVSLVRAPevpVIAGAFC 144
Cdd:PRK12444   37 KKAVAGKVNDKLYDLRRNLEEDAEVEIITIDSNEGVEI---ARHSAAHILAQAVKRLYGD---VNLGVGP---VIENGFY 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938900672 145 YDVVLDKRLdewmpTKENLHSFTKDARALIYKDLPFETLEVEAKVALEIFQ--HNKYKLDFIEEKASqnpERIVKLHRFG 222
Cdd:PRK12444  108 YDMDLPSSV-----NVEDLRKIEKEMKKIINENIKIERVEVSREEAAKLFQemNDRLKLELLEAIPS---GESITLYKQG 179

                         170
                  ....*....|....
gi 1938900672 223 DFIDVSEGPLIPRT 236
Cdd:PRK12444  180 EFVDLCRGPHLPST 193
Ubiquitin_like_fold cd00196
Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various ...
 33-91 9.89e-06

Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. The ubiquitination process comprises a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a ubiquitin-like manner but with biochemically distinct roles. Ubiquitin and ubiquitin-like proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some other ubiquitin-like domains have adaptor roles in ubiquitin-signaling by mediating protein-protein interaction. In addition to Ubiquitin-like (Ubl) domain, Ras-associating (RA) domain, F0/F1 sub-domain of FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, TGS (ThrRS, GTPase and SpoT) domain, Ras-binding domain (RBD), Ubiquitin regulatory domain X (UBX), Dublecortin-like domain, and RING finger- and WD40-associated ubiquitin-like (RAWUL) domain have beta-grasp ubiquitin-like folds, and are included in this superfamily.


Pssm-ID: 340450  Cd Length: 68  Bit Score: 42.69  E-value: 9.89e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1938900672  33 HVGKTDPGTVFVMNKNiSTPYSCAMHLSEWY--CRKSILALVDGQPWDMYKP-----LTKSCEIKF 91
Cdd:cd00196     3 VETPSLKKIVVAVPPS-TTLRQVLEKVAKRIglPPDVIRLLFNGQVLDDLMTakqvgLEPGEELHF 67
TGS pfam02824
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain ...
 50-93 4.29e-03

TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organizm, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.


Pssm-ID: 427005 [Multi-domain]  Cd Length: 60  Bit Score: 34.83  E-value: 4.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1938900672  50 STPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFLT 93
Cdd:pfam02824  17 ATPEDFAYAIHTSLAKKFIYAKVNGQLVGLDHPLEDGDVVEIVT 60
 
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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