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Conserved domains on  [gi|16741492|gb|AAH16561|]
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Mitochondrial ribosomal protein L39 [Mus musculus]

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
 2-231 2.69e-28

threonyl-tRNA synthetase


The actual alignment was detected with superfamily member PLN02908:

Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 114.48  E-value: 2.69e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492    2 RNDLFNREKSRQLSltpRTEKIEVKHVGKTDP-GTVFVMNKNISTPYSCAMHLSEWYCSKSILALVDGQPWDMYKPLTKS 80
Cdd:PLN02908  29 RIELFEKIQARQLA---RLESAGGDPIKVTLPdGAVKDGKKWVTTPMDIAKEISKGLANSALIAQVDGVLWDMTRPLEGD 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492   81 CEIKFLTFKDPDPREVnkaYWRSCAMMLGCVIERAfkddYVVSLLRAPEVPVIAGaFCYDVTLDKR-LDEwmptkENLRS 159
Cdd:PLN02908 106 CKLKLFKFDDDEGRDT---FWHSSAHILGEALELE----YGCKLCIGPCTTRGEG-FYYDAFYGDRtLNE-----EDFKP 172

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16741492  160 FTKDAHALIYRDLPFETLDVDARVALEIFQHNKYKVDFIEEKasqnPE-RIVKLHRIGDFIDVSEGPLIPRTS 231
Cdd:PLN02908 173 IEARAEKAVKEKQPFERIEVTREEALEMFSENKFKVEIINDL----PEdATITVYRCGPLVDLCRGPHIPNTS 241
 
Name Accession Description Interval E-value
PLN02908 PLN02908
threonyl-tRNA synthetase
 2-231 2.69e-28

threonyl-tRNA synthetase


Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 114.48  E-value: 2.69e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492    2 RNDLFNREKSRQLSltpRTEKIEVKHVGKTDP-GTVFVMNKNISTPYSCAMHLSEWYCSKSILALVDGQPWDMYKPLTKS 80
Cdd:PLN02908  29 RIELFEKIQARQLA---RLESAGGDPIKVTLPdGAVKDGKKWVTTPMDIAKEISKGLANSALIAQVDGVLWDMTRPLEGD 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492   81 CEIKFLTFKDPDPREVnkaYWRSCAMMLGCVIERAfkddYVVSLLRAPEVPVIAGaFCYDVTLDKR-LDEwmptkENLRS 159
Cdd:PLN02908 106 CKLKLFKFDDDEGRDT---FWHSSAHILGEALELE----YGCKLCIGPCTTRGEG-FYYDAFYGDRtLNE-----EDFKP 172

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16741492  160 FTKDAHALIYRDLPFETLDVDARVALEIFQHNKYKVDFIEEKasqnPE-RIVKLHRIGDFIDVSEGPLIPRTS 231
Cdd:PLN02908 173 IEARAEKAVKEKQPFERIEVTREEALEMFSENKFKVEIINDL----PEdATITVYRCGPLVDLCRGPHIPNTS 241
TGS cd01616
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; ...
 24-86 2.28e-24

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: 93.05  E-value: 2.28e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16741492  24 EVKHVGKTdPGTVFVMNKnISTPYSCAMHLSEWYCSKSILALVDGQPWDMYKPLTKSCEIKFL 86
Cdd:cd01616   1 EVFTVGKT-PGTVFVMNK-GATAYSCAMHLHEDYCRKSILALVDGQLWDMYYPLTKGDEIKFL 61
ThrS COG0441
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA ...
 60-233 2.85e-20

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: 90.48  E-value: 2.85e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492  60 KSILALVDGQPWDMYKPLTKSCEIKFLTFKDPDPREVnkaYWRSCAMMLGCVIERAFkddyvvsllraPEV-----PVIA 134
Cdd:COG0441  34 AAVAAKVNGELVDLSTPIEEDAELEIVTFDDEEGLEI---LRHSAAHLLAQAVKRLY-----------PDAkltigPVIE 99

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492 135 GAFCYDVTLDKRLdewmpTKENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQ--HNKYKVDFIEEKASqnpERIVKL 212
Cdd:COG0441 100 NGFYYDFDLERPF-----TPEDLEKIEKEMKEIIKEDLPIEREEVSREEAIELFKekGEPYKVELIEDIPE---DEEISL 171

                       170       180
                ....*....|....*....|.
gi 16741492 213 HRIGDFIDVSEGPLIPRTSVC 233
Cdd:COG0441 172 YRQGEFVDLCRGPHVPSTGKI 192
TGS pfam02824
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain ...
 44-87 9.13e-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: 34.06  E-value: 9.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 16741492    44 STPYSCAMHLSEWYCSKSILALVDGQPWDMYKPLTKSCEIKFLT 87
Cdd:pfam02824  17 ATPEDFAYAIHTSLAKKFIYAKVNGQLVGLDHPLEDGDVVEIVT 60
 
Name Accession Description Interval E-value
PLN02908 PLN02908
threonyl-tRNA synthetase
 2-231 2.69e-28

threonyl-tRNA synthetase


Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 114.48  E-value: 2.69e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492    2 RNDLFNREKSRQLSltpRTEKIEVKHVGKTDP-GTVFVMNKNISTPYSCAMHLSEWYCSKSILALVDGQPWDMYKPLTKS 80
Cdd:PLN02908  29 RIELFEKIQARQLA---RLESAGGDPIKVTLPdGAVKDGKKWVTTPMDIAKEISKGLANSALIAQVDGVLWDMTRPLEGD 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492   81 CEIKFLTFKDPDPREVnkaYWRSCAMMLGCVIERAfkddYVVSLLRAPEVPVIAGaFCYDVTLDKR-LDEwmptkENLRS 159
Cdd:PLN02908 106 CKLKLFKFDDDEGRDT---FWHSSAHILGEALELE----YGCKLCIGPCTTRGEG-FYYDAFYGDRtLNE-----EDFKP 172

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16741492  160 FTKDAHALIYRDLPFETLDVDARVALEIFQHNKYKVDFIEEKasqnPE-RIVKLHRIGDFIDVSEGPLIPRTS 231
Cdd:PLN02908 173 IEARAEKAVKEKQPFERIEVTREEALEMFSENKFKVEIINDL----PEdATITVYRCGPLVDLCRGPHIPNTS 241
TGS cd01616
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; ...
 24-86 2.28e-24

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: 93.05  E-value: 2.28e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16741492  24 EVKHVGKTdPGTVFVMNKnISTPYSCAMHLSEWYCSKSILALVDGQPWDMYKPLTKSCEIKFL 86
Cdd:cd01616   1 EVFTVGKT-PGTVFVMNK-GATAYSCAMHLHEDYCRKSILALVDGQLWDMYYPLTKGDEIKFL 61
ThrS COG0441
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA ...
 60-233 2.85e-20

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: 90.48  E-value: 2.85e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492  60 KSILALVDGQPWDMYKPLTKSCEIKFLTFKDPDPREVnkaYWRSCAMMLGCVIERAFkddyvvsllraPEV-----PVIA 134
Cdd:COG0441  34 AAVAAKVNGELVDLSTPIEEDAELEIVTFDDEEGLEI---LRHSAAHLLAQAVKRLY-----------PDAkltigPVIE 99

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492 135 GAFCYDVTLDKRLdewmpTKENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQ--HNKYKVDFIEEKASqnpERIVKL 212
Cdd:COG0441 100 NGFYYDFDLERPF-----TPEDLEKIEKEMKEIIKEDLPIEREEVSREEAIELFKekGEPYKVELIEDIPE---DEEISL 171

                       170       180
                ....*....|....*....|.
gi 16741492 213 HRIGDFIDVSEGPLIPRTSVC 233
Cdd:COG0441 172 YRQGEFVDLCRGPHVPSTGKI 192
TGS_ThrRS cd01667
TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar ...
 34-92 1.20e-19

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: 80.61  E-value: 1.20e-19
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 16741492  34 GTVFVMNKNIsTPYSCAMHLSEWYCSKSILALVDGQPWDMYKPLTKSCEIKFLTFKDPD 92
Cdd:cd01667   8 GSVKEFPKGT-TPLDIAKSISPGLAKKAVAAKVNGELVDLSRPLEEDAELEILTFDDPE 65
PRK12444 PRK12444
threonyl-tRNA synthetase; Reviewed
 60-230 1.17e-09

threonyl-tRNA synthetase; Reviewed


Pssm-ID: 183530 [Multi-domain]  Cd Length: 639  Bit Score: 58.99  E-value: 1.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492   60 KSILALVDGQPWDMYKPLTKSCEIKFLTFKDPDPREVnkaYWRSCAMMLGCVIERAFKDdyvVSLLRAPevpVIAGAFCY 139
Cdd:PRK12444  38 KAVAGKVNDKLYDLRRNLEEDAEVEIITIDSNEGVEI---ARHSAAHILAQAVKRLYGD---VNLGVGP---VIENGFYY 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16741492  140 DVTLDKRLdewmpTKENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQ--HNKYKVDFIEEKASqnpERIVKLHRIGD 217
Cdd:PRK12444 109 DMDLPSSV-----NVEDLRKIEKEMKKIINENIKIERVEVSREEAAKLFQemNDRLKLELLEAIPS---GESITLYKQGE 180

                        170
                 ....*....|...
gi 16741492  218 FIDVSEGPLIPRT 230
Cdd:PRK12444 181 FVDLCRGPHLPST 193
Ubiquitin_like_fold cd00196
Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various ...
 25-85 3.18e-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: 43.85  E-value: 3.18e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16741492  25 VKHVGKTDPGTVFVMNKNiSTPYSCAMHLSEWY--CSKSILALVDGQPWDMYKP-----LTKSCEIKF 85
Cdd:cd00196   1 VKVETPSLKKIVVAVPPS-TTLRQVLEKVAKRIglPPDVIRLLFNGQVLDDLMTakqvgLEPGEELHF 67
TGS pfam02824
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain ...
 44-87 9.13e-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: 34.06  E-value: 9.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 16741492    44 STPYSCAMHLSEWYCSKSILALVDGQPWDMYKPLTKSCEIKFLT 87
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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