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Conserved domains on  [gi|1958765025|ref|XP_038962167|]
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tubulin polyglutamylase TTLL11 isoform X6 [Rattus norvegicus]

Protein Classification

ATP-grasp domain-containing protein( domain architecture ID 106900)

ATP-grasp domain-containing protein may be related to carbamoyl phosphate synthetase and predicted to be involved in the biosynthesis of a ribonucleoside involved in stress response

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CPSase_L_D2 super family cl17255
Carbamoyl-phosphate synthase L chain, ATP binding domain; Carbamoyl-phosphate synthase ...
 1-261 3.52e-61

Carbamoyl-phosphate synthase L chain, ATP binding domain; Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117. The ATP binding domain (this one) has an ATP-grasp fold.


The actual alignment was detected with superfamily member pfam03133:

Pssm-ID: 473076  Cd Length: 291  Bit Score: 203.34  E-value: 3.52e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025   1 MTEMVRKITLSRALRIMQNLFPEEYNFYPRSWILPEEFQLFVAQVQTVKDNdptwrpTFIVKPDSGCQGDGIYLIKDPCD 80
Cdd:pfam03133  17 SYEITRKDLLWKNIKRTPCDRGLKGDFLPRTFILPTDLAEFVDYFEDRERN------TWIVKPSASARGRGIRVTNKLSQ 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025  81 crLTGTLHNRPAVVQEYIRKPLLIDKLKFDIRLYVLLKSLDPLEIYIAKDGLSRFCTEPYqEPNPQNLHHVFMHLTNYSL 160
Cdd:pfam03133  91 --IPKWSQSRPLVVQKYIERPLLIDGRKFDIRLYVLVTSVNPLRVYVYREGLLRFASVKY-SPSSSDLDDVEMHLTNYSI 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025 161 NIHSGKFVHSDSASTGSKRTFSSILCRLSSKGVDikKVWSDIISLVIKTVIAltpelkVFYQSDIPTGRPGPTCFQILGF 240
Cdd:pfam03133 168 QKKSSSLNEDYNEPHGHKWSLQNFWKYLEEKDKD--EIWLEIESIIIKTILA------AEVEASRLNVQPLPNCFELYGF 239

                         250       260
                  ....*....|....*....|.
gi 1958765025 241 DILLMKNLKPMLLEVNANPSM 261
Cdd:pfam03133 240 DFMIDENLKPWLLEVNSSPSL 260
 
Name Accession Description Interval E-value
TTL pfam03133
Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several ...
 1-261 3.52e-61

Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain.


Pssm-ID: 397308  Cd Length: 291  Bit Score: 203.34  E-value: 3.52e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025   1 MTEMVRKITLSRALRIMQNLFPEEYNFYPRSWILPEEFQLFVAQVQTVKDNdptwrpTFIVKPDSGCQGDGIYLIKDPCD 80
Cdd:pfam03133  17 SYEITRKDLLWKNIKRTPCDRGLKGDFLPRTFILPTDLAEFVDYFEDRERN------TWIVKPSASARGRGIRVTNKLSQ 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025  81 crLTGTLHNRPAVVQEYIRKPLLIDKLKFDIRLYVLLKSLDPLEIYIAKDGLSRFCTEPYqEPNPQNLHHVFMHLTNYSL 160
Cdd:pfam03133  91 --IPKWSQSRPLVVQKYIERPLLIDGRKFDIRLYVLVTSVNPLRVYVYREGLLRFASVKY-SPSSSDLDDVEMHLTNYSI 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025 161 NIHSGKFVHSDSASTGSKRTFSSILCRLSSKGVDikKVWSDIISLVIKTVIAltpelkVFYQSDIPTGRPGPTCFQILGF 240
Cdd:pfam03133 168 QKKSSSLNEDYNEPHGHKWSLQNFWKYLEEKDKD--EIWLEIESIIIKTILA------AEVEASRLNVQPLPNCFELYGF 239

                         250       260
                  ....*....|....*....|.
gi 1958765025 241 DILLMKNLKPMLLEVNANPSM 261
Cdd:pfam03133 240 DFMIDENLKPWLLEVNSSPSL 260
LysX COG0189
Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily [Amino acid transport ...
 29-116 8.13e-04

Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily [Amino acid transport and metabolism, Coenzyme transport and metabolism, Translation, ribosomal structure and biogenesis, Secondary metabolites biosynthesis, transport and catabolism]; Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 439959 [Multi-domain]  Cd Length: 289  Bit Score: 41.46  E-value: 8.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025  29 PRSWILPEEFQL--FVAQvqtvkdndptWRPTFIVKPDSGCQGDGIYLIKDP------CDcRLTGtLHNRPAVVQEYIRK 100
Cdd:COG0189   112 PPTLVTRDPDDLraFLEE----------LGGPVVLKPLDGSGGRGVFLVEDEdalesiLE-ALTE-LGSEPVLVQEFIPE 179

                          90
                  ....*....|....*.
gi 1958765025 101 pllidKLKFDIRLYVL 116
Cdd:COG0189   180 -----EDGRDIRVLVV 190
 
Name Accession Description Interval E-value
TTL pfam03133
Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several ...
 1-261 3.52e-61

Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain.


Pssm-ID: 397308  Cd Length: 291  Bit Score: 203.34  E-value: 3.52e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025   1 MTEMVRKITLSRALRIMQNLFPEEYNFYPRSWILPEEFQLFVAQVQTVKDNdptwrpTFIVKPDSGCQGDGIYLIKDPCD 80
Cdd:pfam03133  17 SYEITRKDLLWKNIKRTPCDRGLKGDFLPRTFILPTDLAEFVDYFEDRERN------TWIVKPSASARGRGIRVTNKLSQ 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025  81 crLTGTLHNRPAVVQEYIRKPLLIDKLKFDIRLYVLLKSLDPLEIYIAKDGLSRFCTEPYqEPNPQNLHHVFMHLTNYSL 160
Cdd:pfam03133  91 --IPKWSQSRPLVVQKYIERPLLIDGRKFDIRLYVLVTSVNPLRVYVYREGLLRFASVKY-SPSSSDLDDVEMHLTNYSI 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025 161 NIHSGKFVHSDSASTGSKRTFSSILCRLSSKGVDikKVWSDIISLVIKTVIAltpelkVFYQSDIPTGRPGPTCFQILGF 240
Cdd:pfam03133 168 QKKSSSLNEDYNEPHGHKWSLQNFWKYLEEKDKD--EIWLEIESIIIKTILA------AEVEASRLNVQPLPNCFELYGF 239

                         250       260
                  ....*....|....*....|.
gi 1958765025 241 DILLMKNLKPMLLEVNANPSM 261
Cdd:pfam03133 240 DFMIDENLKPWLLEVNSSPSL 260
LysX COG0189
Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily [Amino acid transport ...
 29-116 8.13e-04

Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily [Amino acid transport and metabolism, Coenzyme transport and metabolism, Translation, ribosomal structure and biogenesis, Secondary metabolites biosynthesis, transport and catabolism]; Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 439959 [Multi-domain]  Cd Length: 289  Bit Score: 41.46  E-value: 8.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025  29 PRSWILPEEFQL--FVAQvqtvkdndptWRPTFIVKPDSGCQGDGIYLIKDP------CDcRLTGtLHNRPAVVQEYIRK 100
Cdd:COG0189   112 PPTLVTRDPDDLraFLEE----------LGGPVVLKPLDGSGGRGVFLVEDEdalesiLE-ALTE-LGSEPVLVQEFIPE 179

                          90
                  ....*....|....*.
gi 1958765025 101 pllidKLKFDIRLYVL 116
Cdd:COG0189   180 -----EDGRDIRVLVV 190
ATPgrasp_ST pfam14397
Sugar-transfer associated ATP-grasp; A member of the ATP-grasp fold predicted to be involved ...
 34-263 1.60e-03

Sugar-transfer associated ATP-grasp; A member of the ATP-grasp fold predicted to be involved in the biosynthesis of cell surface polysaccharides.


Pssm-ID: 405145 [Multi-domain]  Cd Length: 278  Bit Score: 40.40  E-value: 1.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025  34 LPEEFQLFV--AQVQTVKDNDPTWRPTFIVKPDSGCQGDGIYLIK------------------DPCDCRLTGTLHNRPAV 93
Cdd:pfam14397  36 VPKLYGVISigHDISRLDAFVRSLPPGFVIKPAKGSGGKGILVITrrgdqdyfkssgcrilldELKRHVSSLGGKPDVAL 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025  94 VQEYIRKPLLIDKLKF----DIRLYVllksldpleiYIAKDGLSRFCTepyqepnpqnlhhvFMHLTNYSL---NIHSGK 166
Cdd:pfam14397 116 VEERIVQDPVFAKLSPesvnTIRVIT----------FLLDNGVPVMPA--------------MLRLGTGASlvdNLHQGG 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958765025 167 -FVHSDSAsTGS--KRTFSSILCRLSSK-----GVDIKKV----WSDIISLViKTVIALTPELKvfyqsdiptgrpgptc 234
Cdd:pfam14397 172 vGVGIDLA-TGVlfKPALQAVQYGEPIEhhpdtGVKFRGFqipnWDQILELA-AECAQTLPGLG---------------- 233

                         250       260
                  ....*....|....*....|....*....
gi 1958765025 235 fqILGFDILLMKNLKPMLLEVNANPSMRI 263
Cdd:pfam14397 234 --YVGWDIVIDENGGPLLLELNARPGLGI 260
 
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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