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Conserved domains on  [gi|42569807|ref|NP_181589|]
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initiator tRNA phosphoribosyl transferase family protein [Arabidopsis thaliana]

Protein Classification

initiator tRNA phosphoribosyl transferase family protein( domain architecture ID 12182565)

initiator tRNA phosphoribosyl transferase family protein similar to Saccharomyces cerevisiae tRNA A64-2'-O-ribosylphosphate transferase (RIT1), a tRNA backbone modifying enzyme that mediates initiator/elongator tRNA discrimination

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rit1_C pfam17184
Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) ...
 23-309 4.79e-155

Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) which modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. The N-terminal domain is the most conserved region of the protein.


:

Pssm-ID: 435771  Cd Length: 273  Bit Score: 442.77  E-value: 4.79e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807    23 IKRRDNSLYNALRSIYQDSIFVHEISLLWPKLPLVANLRCGLWYS--EKFDATCYFKSTDGHTNNLSFNTSRLNLHLPLL 100
Cdd:pfam17184   1 LKRSTLSIYNRLRSILEDAEFVEEVAAAYPGLPLVANERCGSWYVppEKKAGSAYFKSTDGHTGQWSFSTRRLNLHLLPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807   101 AGEKGGCIIIDSTRKGKRFPDSMSKTIPMWSCVVNRSIFNHWNRlcnidagltsdddgdnirklLDKWDCSLHL---PLW 177
Cdd:pfam17184  81 IGEHGGCIIVDSTRRGKRMPDALSKTIPIWCAVLNRALFPRLGK--------------------SLPWDHDLHLftpPSW 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807   178 VSNTERASIEARLDEWTRELDESGADIASLASCLRKPLRPLWVSQKTVIWLNEVPEHDSWDFTPLILVSAS-ASGELQNR 256
Cdd:pfam17184 141 VSASEHAQIEARIPGFVKSLKALGLDLPSLRGKLGKPLRPLWITPGSSLPLPSVDDFTSLDFHPIILCSASrASSEAQDG 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 42569807   257 TSSEFSWNYIPGAGDDEESWARGLSPNVFWTHVDDLIHSGPDLCNQKVAEIVE 309
Cdd:pfam17184 221 VDSRGGFTYIQGAGDDHELWARGLTPDLFWKHKDDLLSTPEDELPELIAELVE 273
Init_tRNA_PT pfam04179
Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in ...
 403-512 5.65e-36

Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. This C-terminal domain shows similarity to dual specificity phosphatases.


:

Pssm-ID: 427764  Cd Length: 110  Bit Score: 129.63  E-value: 5.65e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807   403 HLHLPMKGSKFDRFSISRNLPPAVNFAKLKMSSGK--KVLVCCQDGEDISICVCLAILMSLFNEEGAFDggkSFEEKSIT 480
Cdd:pfam04179   2 YLHLPLPSGKKGSRNLRTALPEIIQFVRSRLSEDKskKILVCCETGKDLSVGVALAILCLLFDDGTLDD---DPSRPQIT 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 42569807   481 KMDMRRMLIFICKYAVNARPSRGNLKQVFGFL 512
Cdd:pfam04179  79 KDDIRQRLAWIITSSPDANPSRATLQSVNSFL 110
 
Name Accession Description Interval E-value
Rit1_C pfam17184
Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) ...
 23-309 4.79e-155

Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) which modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. The N-terminal domain is the most conserved region of the protein.


Pssm-ID: 435771  Cd Length: 273  Bit Score: 442.77  E-value: 4.79e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807    23 IKRRDNSLYNALRSIYQDSIFVHEISLLWPKLPLVANLRCGLWYS--EKFDATCYFKSTDGHTNNLSFNTSRLNLHLPLL 100
Cdd:pfam17184   1 LKRSTLSIYNRLRSILEDAEFVEEVAAAYPGLPLVANERCGSWYVppEKKAGSAYFKSTDGHTGQWSFSTRRLNLHLLPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807   101 AGEKGGCIIIDSTRKGKRFPDSMSKTIPMWSCVVNRSIFNHWNRlcnidagltsdddgdnirklLDKWDCSLHL---PLW 177
Cdd:pfam17184  81 IGEHGGCIIVDSTRRGKRMPDALSKTIPIWCAVLNRALFPRLGK--------------------SLPWDHDLHLftpPSW 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807   178 VSNTERASIEARLDEWTRELDESGADIASLASCLRKPLRPLWVSQKTVIWLNEVPEHDSWDFTPLILVSAS-ASGELQNR 256
Cdd:pfam17184 141 VSASEHAQIEARIPGFVKSLKALGLDLPSLRGKLGKPLRPLWITPGSSLPLPSVDDFTSLDFHPIILCSASrASSEAQDG 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 42569807   257 TSSEFSWNYIPGAGDDEESWARGLSPNVFWTHVDDLIHSGPDLCNQKVAEIVE 309
Cdd:pfam17184 221 VDSRGGFTYIQGAGDDHELWARGLTPDLFWKHKDDLLSTPEDELPELIAELVE 273
Init_tRNA_PT pfam04179
Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in ...
 403-512 5.65e-36

Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. This C-terminal domain shows similarity to dual specificity phosphatases.


Pssm-ID: 427764  Cd Length: 110  Bit Score: 129.63  E-value: 5.65e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807   403 HLHLPMKGSKFDRFSISRNLPPAVNFAKLKMSSGK--KVLVCCQDGEDISICVCLAILMSLFNEEGAFDggkSFEEKSIT 480
Cdd:pfam04179   2 YLHLPLPSGKKGSRNLRTALPEIIQFVRSRLSEDKskKILVCCETGKDLSVGVALAILCLLFDDGTLDD---DPSRPQIT 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 42569807   481 KMDMRRMLIFICKYAVNARPSRGNLKQVFGFL 512
Cdd:pfam04179  79 KDDIRQRLAWIITSSPDANPSRATLQSVNSFL 110
DSP cd14498
dual-specificity phosphatase domain; The dual-specificity phosphatase domain is found in ...
 367-463 1.41e-08

dual-specificity phosphatase domain; The dual-specificity phosphatase domain is found in typical and atypical dual-specificity phosphatases (DUSPs), which function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48). Typical DUSPs, also called mitogen-activated protein kinase (MAPK) phosphatases (MKPs), deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. Atypical DUSPs contain the catalytic dual specificity phosphatase domain but lack the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. Also included in this family are dual specificity phosphatase-like domains of catalytically inactive members such as serine/threonine/tyrosine-interacting protein (STYX) and serine/threonine/tyrosine interacting like 1 (STYXL1), as well as active phosphatases with substrates that are not phosphoproteins such as PTP localized to the mitochondrion 1 (PTPMT1), which is a lipid phosphatase, and laforin, which is a glycogen phosphatase.


Pssm-ID: 350348 [Multi-domain]  Cd Length: 135  Bit Score: 53.32  E-value: 1.41e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807 367 NLAVGASQVAC-----KETSIDCILNCDQNPISVPVSYLEEHLHLPMKGSkfDRFSISRNLPPAVNFAKLKMSSGKKVLV 441
Cdd:cd14498   7 GLYLGSLDAAQdkellKKLGITHILNVAGEPPPNKFPDGIKYLRIPIEDS--PDEDILSHFEEAIEFIEEALKKGGKVLV 84

                        90       100
                ....*....|....*....|..
gi 42569807 442 CCQDGEDISICVCLAILMSLFN 463
Cdd:cd14498  85 HCQAGVSRSATIVIAYLMKKYG 106
DSPc smart00195
Dual specificity phosphatase, catalytic domain;
362-463 1.88e-03

Dual specificity phosphatase, catalytic domain;


Pssm-ID: 214551 [Multi-domain]  Cd Length: 138  Bit Score: 38.80  E-value: 1.88e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807    362 WLSSTNLAVGASQVacKETSIDCILNC-DQNPISVPVSYleEHLHLPMkgSKFDRFSISRNLPPAVNFAKLKMSSGKKVL 440
Cdd:smart00195   9 YLGSYSDALNLALL--KKLGITHVINVtNEVPNYNGSDF--TYLGVPI--DDNTETKISPYFPEAVEFIEDAESKGGKVL 82

                           90       100
                   ....*....|....*....|...
gi 42569807    441 VCCQDGEDISICVCLAILMSLFN 463
Cdd:smart00195  83 VHCQAGVSRSATLIIAYLMKTRN 105
 
Name Accession Description Interval E-value
Rit1_C pfam17184
Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) ...
 23-309 4.79e-155

Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) which modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. The N-terminal domain is the most conserved region of the protein.


Pssm-ID: 435771  Cd Length: 273  Bit Score: 442.77  E-value: 4.79e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807    23 IKRRDNSLYNALRSIYQDSIFVHEISLLWPKLPLVANLRCGLWYS--EKFDATCYFKSTDGHTNNLSFNTSRLNLHLPLL 100
Cdd:pfam17184   1 LKRSTLSIYNRLRSILEDAEFVEEVAAAYPGLPLVANERCGSWYVppEKKAGSAYFKSTDGHTGQWSFSTRRLNLHLLPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807   101 AGEKGGCIIIDSTRKGKRFPDSMSKTIPMWSCVVNRSIFNHWNRlcnidagltsdddgdnirklLDKWDCSLHL---PLW 177
Cdd:pfam17184  81 IGEHGGCIIVDSTRRGKRMPDALSKTIPIWCAVLNRALFPRLGK--------------------SLPWDHDLHLftpPSW 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807   178 VSNTERASIEARLDEWTRELDESGADIASLASCLRKPLRPLWVSQKTVIWLNEVPEHDSWDFTPLILVSAS-ASGELQNR 256
Cdd:pfam17184 141 VSASEHAQIEARIPGFVKSLKALGLDLPSLRGKLGKPLRPLWITPGSSLPLPSVDDFTSLDFHPIILCSASrASSEAQDG 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 42569807   257 TSSEFSWNYIPGAGDDEESWARGLSPNVFWTHVDDLIHSGPDLCNQKVAEIVE 309
Cdd:pfam17184 221 VDSRGGFTYIQGAGDDHELWARGLTPDLFWKHKDDLLSTPEDELPELIAELVE 273
Init_tRNA_PT pfam04179
Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in ...
 403-512 5.65e-36

Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. This C-terminal domain shows similarity to dual specificity phosphatases.


Pssm-ID: 427764  Cd Length: 110  Bit Score: 129.63  E-value: 5.65e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807   403 HLHLPMKGSKFDRFSISRNLPPAVNFAKLKMSSGK--KVLVCCQDGEDISICVCLAILMSLFNEEGAFDggkSFEEKSIT 480
Cdd:pfam04179   2 YLHLPLPSGKKGSRNLRTALPEIIQFVRSRLSEDKskKILVCCETGKDLSVGVALAILCLLFDDGTLDD---DPSRPQIT 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 42569807   481 KMDMRRMLIFICKYAVNARPSRGNLKQVFGFL 512
Cdd:pfam04179  79 KDDIRQRLAWIITSSPDANPSRATLQSVNSFL 110
DSP cd14498
dual-specificity phosphatase domain; The dual-specificity phosphatase domain is found in ...
 367-463 1.41e-08

dual-specificity phosphatase domain; The dual-specificity phosphatase domain is found in typical and atypical dual-specificity phosphatases (DUSPs), which function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48). Typical DUSPs, also called mitogen-activated protein kinase (MAPK) phosphatases (MKPs), deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. Atypical DUSPs contain the catalytic dual specificity phosphatase domain but lack the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. Also included in this family are dual specificity phosphatase-like domains of catalytically inactive members such as serine/threonine/tyrosine-interacting protein (STYX) and serine/threonine/tyrosine interacting like 1 (STYXL1), as well as active phosphatases with substrates that are not phosphoproteins such as PTP localized to the mitochondrion 1 (PTPMT1), which is a lipid phosphatase, and laforin, which is a glycogen phosphatase.


Pssm-ID: 350348 [Multi-domain]  Cd Length: 135  Bit Score: 53.32  E-value: 1.41e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807 367 NLAVGASQVAC-----KETSIDCILNCDQNPISVPVSYLEEHLHLPMKGSkfDRFSISRNLPPAVNFAKLKMSSGKKVLV 441
Cdd:cd14498   7 GLYLGSLDAAQdkellKKLGITHILNVAGEPPPNKFPDGIKYLRIPIEDS--PDEDILSHFEEAIEFIEEALKKGGKVLV 84

                        90       100
                ....*....|....*....|..
gi 42569807 442 CCQDGEDISICVCLAILMSLFN 463
Cdd:cd14498  85 HCQAGVSRSATIVIAYLMKKYG 106
DSPc pfam00782
Dual specificity phosphatase, catalytic domain; Ser/Thr and Tyr protein phosphatases. The ...
 378-463 1.61e-05

Dual specificity phosphatase, catalytic domain; Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a "recognition" region.


Pssm-ID: 395632 [Multi-domain]  Cd Length: 127  Bit Score: 44.56  E-value: 1.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807   378 KETSIDCILNCDQNPISVPVSYLeeHLHLPMKgsKFDRFSISRNLPPAVNFAKLKMSSGKKVLVCCQDGEDISICVCLAI 457
Cdd:pfam00782  15 SKLGITAVINVTREVDLYNSGIL--YLRIPVE--DNHETNISKYLEEAVEFIDDARQKGGKVLVHCQAGISRSATLIIAY 90


                  ....*.
gi 42569807   458 LMSLFN 463
Cdd:pfam00782  91 LMKTRN 96
DSPc smart00195
Dual specificity phosphatase, catalytic domain;
362-463 1.88e-03

Dual specificity phosphatase, catalytic domain;


Pssm-ID: 214551 [Multi-domain]  Cd Length: 138  Bit Score: 38.80  E-value: 1.88e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807    362 WLSSTNLAVGASQVacKETSIDCILNC-DQNPISVPVSYleEHLHLPMkgSKFDRFSISRNLPPAVNFAKLKMSSGKKVL 440
Cdd:smart00195   9 YLGSYSDALNLALL--KKLGITHVINVtNEVPNYNGSDF--TYLGVPI--DDNTETKISPYFPEAVEFIEDAESKGGKVL 82

                           90       100
                   ....*....|....*....|...
gi 42569807    441 VCCQDGEDISICVCLAILMSLFN 463
Cdd:smart00195  83 VHCQAGVSRSATLIIAYLMKTRN 105
DSP_STYXL1 cd14517
dual specificity phosphatase-like domain of serine/threonine/tyrosine interacting like 1; ...
 368-507 2.21e-03

dual specificity phosphatase-like domain of serine/threonine/tyrosine interacting like 1; Serine/threonine/tyrosine interacting like 1 (STYXL1), also known as DUSP24 and MK-STYX, is a catalytically inactive phosphatase with homology to the mitogen-activated protein kinase (MAPK) phosphatases (MKPs). STYXL1 plays a role in regulating pathways by competing with active phosphatases for binding to MAPKs. Similar to MKPs, STYXL1 contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, however its C-terminal dual specificity phosphatase-like domain is a pseudophosphatase missing the catalytic cysteine.


Pssm-ID: 350367 [Multi-domain]  Cd Length: 155  Bit Score: 38.80  E-value: 2.21e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569807 368 LAVGASQVAC-----KETSIDCILNCDQNPISVPVSYLEEHLHLPMKGS-KFDRFSisrNLPPAVNFAKLKMSSGKKVLV 441
Cdd:cd14517  19 LYMGNYKQACdkkiqKDLKIKAHINVSMDADELFKSGNDQVLHIPVEDSvEADLLS---FFERACSFIDKHKNNGSRVLV 95

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 42569807 442 CCQDGEDISICVCLAILMSLFneegafdggksfeeksitKMDMRRMLIFICKYAVNARPSRGNLKQ 507
Cdd:cd14517  96 FSTLGISRSVAVAIAYLMYHY------------------KWSLKDAWKYLLKCKNNMRPNRGFVKQ 143
 
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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