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Conserved domains on  [gi|79324827|ref|NP_001031519|]
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initiator tRNA phosphoribosyl transferase family protein [Arabidopsis thaliana]

Protein Classification

dual specificity protein phosphatase family protein; phosphatase PAP2/dual specificity phosphatase family protein( domain architecture ID 13878237)

dual specificity protein phosphatase family protein such as dual specificity phosphatases, which dephosphorylate phosphotyrosine, phosphoserine, and phosphothreonine residues, as well as tyrosine-specific protein phosphatases| bifunctional phosphatase PAP2/dual specificity phosphatase (DSP) family protein containing a C-terminal DSP domain that may dephosphorylate phosphotyrosine, phosphoserine, and phosphothreonine residues in target proteins, and an N-terminal phosphatase PAP2 domain that may be a histidine phosphatase that catalyzes the dephosphorylation of phospholipids

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 5.77e-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: 440.46  E-value: 5.77e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827    23 IKRRDNSLYNALRSIYQDSIFVHEISLLWPKLPLVANLRCGLWYS--EKFDATCYFKSTDGHTNNLSFNTSRLNLHLPLL 100
Cdd:pfam17184   1 LKRSTLSIYNRLRSILEDAEFVEEVAAAYPGLPLVANERCGSWYVppEKKAGSAYFKSTDGHTGQWSFSTRRLNLHLLPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827   101 AGEKGGCIIIDSTRKGKRFPDSMSKTIPMWSCVVNRSIFNHWNRlcnidagltsdddgdnirklLDKWDCSLHL---PLW 177
Cdd:pfam17184  81 IGEHGGCIIVDSTRRGKRMPDALSKTIPIWCAVLNRALFPRLGK--------------------SLPWDHDLHLftpPSW 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827   178 VSNTERASIEARLDEWTRELDESGADIASLASCLRKPLRPLWVSQKTVIWLNEVPEHDSWDFTPLILVSAS-ASGELQNR 256
Cdd:pfam17184 141 VSASEHAQIEARIPGFVKSLKALGLDLPSLRGKLGKPLRPLWITPGSSLPLPSVDDFTSLDFHPIILCSASrASSEAQDG 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 79324827   257 TSSEFSWNYIPGAGDDEESWARGLSPNVFWTHVDDLIHSGPDLCNQKVAEIVE 309
Cdd:pfam17184 221 VDSRGGFTYIQGAGDDHELWARGLTPDLFWKHKDDLLSTPEDELPELIAELVE 273
PTP_DSP_cys super family cl28904
cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily; This ...
 403-447 4.00e-09

cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily; This superfamily is composed of cys-based phosphatases, which includes classical protein tyrosine phosphatases (PTPs) as well as dual-specificity phosphatases (DUSPs or DSPs). They are characterized by a CxxxxxR conserved catalytic loop (where C is the catalytic cysteine, x is any amino acid, and R is an arginine). PTPs are part of the tyrosine phosphorylation/dephosphorylation regulatory mechanism, and are important in the response of the cells to physiologic and pathologic changes in their environment. DUSPs show more substrate diversity (including RNA and lipids) and include pTyr, pSer, and pThr phosphatases.


The actual alignment was detected with superfamily member pfam04179:

Pssm-ID: 475123  Cd Length: 110  Bit Score: 54.13  E-value: 4.00e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 79324827   403 HLHLPMKGSKFDRFSISRNLPPAVNFAKLKMSSG--KKVLVCCQDGK 447
Cdd:pfam04179   2 YLHLPLPSGKKGSRNLRTALPEIIQFVRSRLSEDksKKILVCCETGK 48
 
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 5.77e-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: 440.46  E-value: 5.77e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827    23 IKRRDNSLYNALRSIYQDSIFVHEISLLWPKLPLVANLRCGLWYS--EKFDATCYFKSTDGHTNNLSFNTSRLNLHLPLL 100
Cdd:pfam17184   1 LKRSTLSIYNRLRSILEDAEFVEEVAAAYPGLPLVANERCGSWYVppEKKAGSAYFKSTDGHTGQWSFSTRRLNLHLLPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827   101 AGEKGGCIIIDSTRKGKRFPDSMSKTIPMWSCVVNRSIFNHWNRlcnidagltsdddgdnirklLDKWDCSLHL---PLW 177
Cdd:pfam17184  81 IGEHGGCIIVDSTRRGKRMPDALSKTIPIWCAVLNRALFPRLGK--------------------SLPWDHDLHLftpPSW 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827   178 VSNTERASIEARLDEWTRELDESGADIASLASCLRKPLRPLWVSQKTVIWLNEVPEHDSWDFTPLILVSAS-ASGELQNR 256
Cdd:pfam17184 141 VSASEHAQIEARIPGFVKSLKALGLDLPSLRGKLGKPLRPLWITPGSSLPLPSVDDFTSLDFHPIILCSASrASSEAQDG 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 79324827   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 ...
 403-447 4.00e-09

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: 54.13  E-value: 4.00e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 79324827   403 HLHLPMKGSKFDRFSISRNLPPAVNFAKLKMSSG--KKVLVCCQDGK 447
Cdd:pfam04179   2 YLHLPLPSGKKGSRNLRTALPEIIQFVRSRLSEDksKKILVCCETGK 48
DSP cd14498
dual-specificity phosphatase domain; The dual-specificity phosphatase domain is found in ...
 367-447 2.32e-06

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: 46.77  E-value: 2.32e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827 367 NLAVGASQVAC-----KETSIDCILNCDQNPISVPVSYLEEHLHLPMKGSkfDRFSISRNLPPAVNFAKLKMSSGKKVLV 441
Cdd:cd14498   7 GLYLGSLDAAQdkellKKLGITHILNVAGEPPPNKFPDGIKYLRIPIEDS--PDEDILSHFEEAIEFIEEALKKGGKVLV 84


                ....*.
gi 79324827 442 CCQDGK 447
Cdd:cd14498  85 HCQAGV 90
 
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 5.77e-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: 440.46  E-value: 5.77e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827    23 IKRRDNSLYNALRSIYQDSIFVHEISLLWPKLPLVANLRCGLWYS--EKFDATCYFKSTDGHTNNLSFNTSRLNLHLPLL 100
Cdd:pfam17184   1 LKRSTLSIYNRLRSILEDAEFVEEVAAAYPGLPLVANERCGSWYVppEKKAGSAYFKSTDGHTGQWSFSTRRLNLHLLPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827   101 AGEKGGCIIIDSTRKGKRFPDSMSKTIPMWSCVVNRSIFNHWNRlcnidagltsdddgdnirklLDKWDCSLHL---PLW 177
Cdd:pfam17184  81 IGEHGGCIIVDSTRRGKRMPDALSKTIPIWCAVLNRALFPRLGK--------------------SLPWDHDLHLftpPSW 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827   178 VSNTERASIEARLDEWTRELDESGADIASLASCLRKPLRPLWVSQKTVIWLNEVPEHDSWDFTPLILVSAS-ASGELQNR 256
Cdd:pfam17184 141 VSASEHAQIEARIPGFVKSLKALGLDLPSLRGKLGKPLRPLWITPGSSLPLPSVDDFTSLDFHPIILCSASrASSEAQDG 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 79324827   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 ...
 403-447 4.00e-09

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: 54.13  E-value: 4.00e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 79324827   403 HLHLPMKGSKFDRFSISRNLPPAVNFAKLKMSSG--KKVLVCCQDGK 447
Cdd:pfam04179   2 YLHLPLPSGKKGSRNLRTALPEIIQFVRSRLSEDksKKILVCCETGK 48
DSP cd14498
dual-specificity phosphatase domain; The dual-specificity phosphatase domain is found in ...
 367-447 2.32e-06

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: 46.77  E-value: 2.32e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79324827 367 NLAVGASQVAC-----KETSIDCILNCDQNPISVPVSYLEEHLHLPMKGSkfDRFSISRNLPPAVNFAKLKMSSGKKVLV 441
Cdd:cd14498   7 GLYLGSLDAAQdkellKKLGITHILNVAGEPPPNKFPDGIKYLRIPIEDS--PDEDILSHFEEAIEFIEEALKKGGKVLV 84


                ....*.
gi 79324827 442 CCQDGK 447
Cdd:cd14498  85 HCQAGV 90
 
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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