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Conserved domains on  [gi|578836607|ref|XP_006724089|]
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large ribosomal subunit protein mL39 isoform X2 [Homo sapiens]

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
 44-303 3.28e-27

threonyl-tRNA synthetase


The actual alignment was detected with superfamily member PLN02908:

Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 112.56  E-value: 3.28e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607  44 RNDLFNKEKARQLSltpRTEKIEVKHVGKTDP-GTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKS 122
Cdd:PLN02908  29 RIELFEKIQARQLA---RLESAGGDPIKVTLPdGAVKDGKKWVTTPMDIAKEISKGLANSALIAQVDGVLWDMTRPLEGD 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 123 CEIKFLTFKDcdpGEVNKAYWRSCAMMMGCVIERafkdEYMVNLVRAPEVPVISGaFCYDVVL-DSKLDEwmptkENLRS 201
Cdd:PLN02908 106 CKLKLFKFDD---DEGRDTFWHSSAHILGEALEL----EYGCKLCIGPCTTRGEG-FYYDAFYgDRTLNE-----EDFKP 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 202 FTKDAHALIYKDLPFETLEVEAKVALEIFQHSKYKVDFIEEKasqnPE-RIVKLHRIGDFIDVSEGPLIPRTSI-----C 275
Cdd:PLN02908 173 IEARAEKAVKEKQPFERIEVTREEALEMFSENKFKVEIINDL----PEdATITVYRCGPLVDLCRGPHIPNTSFvkafaC 248

                        250       260
                 ....*....|....*....|....*...
gi 578836607 276 FQyeVSAVHNLQPTQPSLIRRFQGVSLP 303
Cdd:PLN02908 249 LK--ASSAYWRGDVDRESLQRVYGISFP 274
 
Name Accession Description Interval E-value
PLN02908 PLN02908
threonyl-tRNA synthetase
 44-303 3.28e-27

threonyl-tRNA synthetase


Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 112.56  E-value: 3.28e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607  44 RNDLFNKEKARQLSltpRTEKIEVKHVGKTDP-GTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKS 122
Cdd:PLN02908  29 RIELFEKIQARQLA---RLESAGGDPIKVTLPdGAVKDGKKWVTTPMDIAKEISKGLANSALIAQVDGVLWDMTRPLEGD 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 123 CEIKFLTFKDcdpGEVNKAYWRSCAMMMGCVIERafkdEYMVNLVRAPEVPVISGaFCYDVVL-DSKLDEwmptkENLRS 201
Cdd:PLN02908 106 CKLKLFKFDD---DEGRDTFWHSSAHILGEALEL----EYGCKLCIGPCTTRGEG-FYYDAFYgDRTLNE-----EDFKP 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 202 FTKDAHALIYKDLPFETLEVEAKVALEIFQHSKYKVDFIEEKasqnPE-RIVKLHRIGDFIDVSEGPLIPRTSI-----C 275
Cdd:PLN02908 173 IEARAEKAVKEKQPFERIEVTREEALEMFSENKFKVEIINDL----PEdATITVYRCGPLVDLCRGPHIPNTSFvkafaC 248

                        250       260
                 ....*....|....*....|....*...
gi 578836607 276 FQyeVSAVHNLQPTQPSLIRRFQGVSLP 303
Cdd:PLN02908 249 LK--ASSAYWRGDVDRESLQRVYGISFP 274
TGS cd01616
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; ...
 66-128 3.13e-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: 93.82  E-value: 3.13e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578836607  66 EVKHVGKTdPGTVFVMNKnISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFL 128
Cdd:cd01616    1 EVFTVGKT-PGTVFVMNK-GATAYSCAMHLHEDYCRKSILALVDGQLWDMYYPLTKGDEIKFL 61
ThrS COG0441
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA ...
 101-275 6.37e-18

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: 84.70  E-value: 6.37e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 101 RKSILALVDGQPWDMYKPLTKSCEIKFLTFKDcDPGEvnKAYWRSCAMMMGCVIERAFkdeymvnlvraPEV-----PVI 175
Cdd:COG0441   33 KAAVAAKVNGELVDLSTPIEEDAELEIVTFDD-EEGL--EILRHSAAHLLAQAVKRLY-----------PDAkltigPVI 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 176 SGAFCYDVVLDSKLdewmpTKENLRSFTKDAHALIYKDLPFETLEVEAKVALEIFQHS--KYKVDFIEEKASqnpERIVK 253
Cdd:COG0441   99 ENGFYYDFDLERPF-----TPEDLEKIEKEMKEIIKEDLPIEREEVSREEAIELFKEKgePYKVELIEDIPE---DEEIS 170

                        170       180
                 ....*....|....*....|..
gi 578836607 254 LHRIGDFIDVSEGPLIPRTSIC 275
Cdd:COG0441  171 LYRQGEFVDLCRGPHVPSTGKI 192
TGS pfam02824
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain ...
 86-129 5.08e-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: 5.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 578836607   86 STPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFLT 129
Cdd:pfam02824  17 ATPEDFAYAIHTSLAKKFIYAKVNGQLVGLDHPLEDGDVVEIVT 60
 
Name Accession Description Interval E-value
PLN02908 PLN02908
threonyl-tRNA synthetase
 44-303 3.28e-27

threonyl-tRNA synthetase


Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 112.56  E-value: 3.28e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607  44 RNDLFNKEKARQLSltpRTEKIEVKHVGKTDP-GTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKS 122
Cdd:PLN02908  29 RIELFEKIQARQLA---RLESAGGDPIKVTLPdGAVKDGKKWVTTPMDIAKEISKGLANSALIAQVDGVLWDMTRPLEGD 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 123 CEIKFLTFKDcdpGEVNKAYWRSCAMMMGCVIERafkdEYMVNLVRAPEVPVISGaFCYDVVL-DSKLDEwmptkENLRS 201
Cdd:PLN02908 106 CKLKLFKFDD---DEGRDTFWHSSAHILGEALEL----EYGCKLCIGPCTTRGEG-FYYDAFYgDRTLNE-----EDFKP 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 202 FTKDAHALIYKDLPFETLEVEAKVALEIFQHSKYKVDFIEEKasqnPE-RIVKLHRIGDFIDVSEGPLIPRTSI-----C 275
Cdd:PLN02908 173 IEARAEKAVKEKQPFERIEVTREEALEMFSENKFKVEIINDL----PEdATITVYRCGPLVDLCRGPHIPNTSFvkafaC 248

                        250       260
                 ....*....|....*....|....*...
gi 578836607 276 FQyeVSAVHNLQPTQPSLIRRFQGVSLP 303
Cdd:PLN02908 249 LK--ASSAYWRGDVDRESLQRVYGISFP 274
TGS cd01616
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; ...
 66-128 3.13e-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: 93.82  E-value: 3.13e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578836607  66 EVKHVGKTdPGTVFVMNKnISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFL 128
Cdd:cd01616    1 EVFTVGKT-PGTVFVMNK-GATAYSCAMHLHEDYCRKSILALVDGQLWDMYYPLTKGDEIKFL 61
TGS_ThrRS cd01667
TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar ...
 76-132 2.29e-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: 2.29e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 578836607  76 GTVFVMNKNIsTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFLTFKD 132
Cdd:cd01667    8 GSVKEFPKGT-TPLDIAKSISPGLAKKAVAAKVNGELVDLSRPLEEDAELEILTFDD 63
ThrS COG0441
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA ...
 101-275 6.37e-18

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: 84.70  E-value: 6.37e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 101 RKSILALVDGQPWDMYKPLTKSCEIKFLTFKDcDPGEvnKAYWRSCAMMMGCVIERAFkdeymvnlvraPEV-----PVI 175
Cdd:COG0441   33 KAAVAAKVNGELVDLSTPIEEDAELEIVTFDD-EEGL--EILRHSAAHLLAQAVKRLY-----------PDAkltigPVI 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 176 SGAFCYDVVLDSKLdewmpTKENLRSFTKDAHALIYKDLPFETLEVEAKVALEIFQHS--KYKVDFIEEKASqnpERIVK 253
Cdd:COG0441   99 ENGFYYDFDLERPF-----TPEDLEKIEKEMKEIIKEDLPIEREEVSREEAIELFKEKgePYKVELIEDIPE---DEEIS 170

                        170       180
                 ....*....|....*....|..
gi 578836607 254 LHRIGDFIDVSEGPLIPRTSIC 275
Cdd:COG0441  171 LYRQGEFVDLCRGPHVPSTGKI 192
PRK12444 PRK12444
threonyl-tRNA synthetase; Reviewed
 101-272 1.35e-10

threonyl-tRNA synthetase; Reviewed


Pssm-ID: 183530 [Multi-domain]  Cd Length: 639  Bit Score: 62.46  E-value: 1.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 101 RKSILALVDGQPWDMYKPLTKSCEIKFLTFkdcDPGEVNKAYWRSCAMMMGCVIERAFKDeymVNLVRAPevpVISGAFC 180
Cdd:PRK12444  37 KKAVAGKVNDKLYDLRRNLEEDAEVEIITI---DSNEGVEIARHSAAHILAQAVKRLYGD---VNLGVGP---VIENGFY 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578836607 181 YDVVLDSKLdewmpTKENLRSFTKDAHALIYKDLPFETLEVEAKVALEIFQ--HSKYKVDFIEEKASqnpERIVKLHRIG 258
Cdd:PRK12444 108 YDMDLPSSV-----NVEDLRKIEKEMKKIINENIKIERVEVSREEAAKLFQemNDRLKLELLEAIPS---GESITLYKQG 179

                        170
                 ....*....|....
gi 578836607 259 DFIDVSEGPLIPRT 272
Cdd:PRK12444 180 EFVDLCRGPHLPST 193
Ubiquitin_like_fold cd00196
Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various ...
 67-127 3.19e-07

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: 46.93  E-value: 3.19e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578836607  67 VKHVGKTDPGTVFVMNKNiSTPYSCAMHLSEWY--CRKSILALVDGQPWDMYKP-----LTKSCEIKF 127
Cdd:cd00196    1 VKVETPSLKKIVVAVPPS-TTLRQVLEKVAKRIglPPDVIRLLFNGQVLDDLMTakqvgLEPGEELHF 67
TGS pfam02824
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain ...
 86-129 5.08e-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: 5.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 578836607   86 STPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLTKSCEIKFLT 129
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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