NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1443061532|ref|XP_015623116|]
View 

proteinaceous RNase P 1, chloroplastic/mitochondrial isoform X2 [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 205-474 1.42e-76

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


:

Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 243.84  E-value: 1.42e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 205 EVKLRVELDMCSKRGDVIGAINLYDSAVKEGIKMGQHHYSVLLYLCSSAALGFvqpaksgnagsgiasigqlhssstqsv 284
Cdd:pfam17177  11 ESELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADAT--------------------------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 285 gnlegddvqseghsedqegnktdlfasddgtekpsripvsDELREYARTRGFEIFEKMRSEeeKVPMNESALTAVARMAM 364
Cdd:pfam17177  64 ----------------------------------------DLKPQLAADRGFEVFEAMKAQ--GVSPNEATYTAVARLAA 101

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 365 SMGNGDMAFDVVKQMKDQGIAPKLRSYGPALTAFCNSGNVEKAFEVEAHMLESGVRPEEPELETLLKASVAAQQGDKVYY 444
Cdd:pfam17177 102 AKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYA 181

                         250       260       270
                  ....*....|....*....|....*....|
gi 1443061532 445 LLHKFRTTVRQASSTTAKLLEDWFQSPTAS 474
Cdd:pfam17177 182 YLHRLRDAVRQVSESTAGVLEEWFRSEAAA 211
PRORP super family cl46281
Protein-only RNase P; PRORPs (protein-only RNase P) are a class of RNA processing enzymes that ...
 515-652 7.46e-47

Protein-only RNase P; PRORPs (protein-only RNase P) are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. Arabidopsis thaliana contains PRORP enzymes (PRORP1, PRORP2 and PRORP3) where PRORP1 localizes to mitochondria as well as chloroplasts, while PRORP2 and PRORP3 are found in the nucleus. In humans and most other metazoans, mt-RNase P is composed of three protein subunits (mitochondrial RNase P proteins 1-3; MRPP1-3), homologs to the Arabidopsis thaliana PRORP1-3. This domain corresponds to the metallonuclease domain of PRORPs. PRORP1 has 22% sequence identity to the human homolog MRPP3. PRORP1 crystal structure shows a V-shaped tripartite structure with a C-terminal metallonuclease domain of the NYN (N4BL1, YacP-like nuclease) family, with a typical and functional two-metal-ion catalytic site that has conserved aspartate residues.


The actual alignment was detected with superfamily member pfam16953:

Pssm-ID: 465320  Cd Length: 242  Bit Score: 165.60  E-value: 7.46e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 515 IDRNGACLACGEKLTIIDLDPKETEDFATLVAKLAIKRERR------SNFDNFQKWLEKHGPFDAVVDGANV-GLFSHKH 587
Cdd:pfam16953   1 IDKSGKCSSCGEKLESIDLSPEETENLAESVLRLVIIREDVfrkttpQEFNRFQKFLERTGPFDAVIDGLNVaGLFGQKR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1443061532 588 ISLSKINIVADVIRQrFQSRKLPLIVVHNRHLTGERMQKpsNRKLVEKWKLSNAIYATPTGSNDD 652
Cdd:pfam16953  81 FSIQQANNVVNVVRQ-LAPQKLRLLVLGRKHMLGGPSNW--NKALMEKWQNAAALFFTPNGSNDD 142
 
Name Accession Description Interval E-value
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 205-474 1.42e-76

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 243.84  E-value: 1.42e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 205 EVKLRVELDMCSKRGDVIGAINLYDSAVKEGIKMGQHHYSVLLYLCSSAALGFvqpaksgnagsgiasigqlhssstqsv 284
Cdd:pfam17177  11 ESELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADAT--------------------------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 285 gnlegddvqseghsedqegnktdlfasddgtekpsripvsDELREYARTRGFEIFEKMRSEeeKVPMNESALTAVARMAM 364
Cdd:pfam17177  64 ----------------------------------------DLKPQLAADRGFEVFEAMKAQ--GVSPNEATYTAVARLAA 101

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 365 SMGNGDMAFDVVKQMKDQGIAPKLRSYGPALTAFCNSGNVEKAFEVEAHMLESGVRPEEPELETLLKASVAAQQGDKVYY 444
Cdd:pfam17177 102 AKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYA 181

                         250       260       270
                  ....*....|....*....|....*....|
gi 1443061532 445 LLHKFRTTVRQASSTTAKLLEDWFQSPTAS 474
Cdd:pfam17177 182 YLHRLRDAVRQVSESTAGVLEEWFRSEAAA 211
PRORP pfam16953
Protein-only RNase P; PRORPs (protein-only RNase P) are a class of RNA processing enzymes that ...
 515-652 7.46e-47

Protein-only RNase P; PRORPs (protein-only RNase P) are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. Arabidopsis thaliana contains PRORP enzymes (PRORP1, PRORP2 and PRORP3) where PRORP1 localizes to mitochondria as well as chloroplasts, while PRORP2 and PRORP3 are found in the nucleus. In humans and most other metazoans, mt-RNase P is composed of three protein subunits (mitochondrial RNase P proteins 1-3; MRPP1-3), homologs to the Arabidopsis thaliana PRORP1-3. This domain corresponds to the metallonuclease domain of PRORPs. PRORP1 has 22% sequence identity to the human homolog MRPP3. PRORP1 crystal structure shows a V-shaped tripartite structure with a C-terminal metallonuclease domain of the NYN (N4BL1, YacP-like nuclease) family, with a typical and functional two-metal-ion catalytic site that has conserved aspartate residues.


Pssm-ID: 465320  Cd Length: 242  Bit Score: 165.60  E-value: 7.46e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 515 IDRNGACLACGEKLTIIDLDPKETEDFATLVAKLAIKRERR------SNFDNFQKWLEKHGPFDAVVDGANV-GLFSHKH 587
Cdd:pfam16953   1 IDKSGKCSSCGEKLESIDLSPEETENLAESVLRLVIIREDVfrkttpQEFNRFQKFLERTGPFDAVIDGLNVaGLFGQKR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1443061532 588 ISLSKINIVADVIRQrFQSRKLPLIVVHNRHLTGERMQKpsNRKLVEKWKLSNAIYATPTGSNDD 652
Cdd:pfam16953  81 FSIQQANNVVNVVRQ-LAPQKLRLLVLGRKHMLGGPSNW--NKALMEKWQNAAALFFTPNGSNDD 142
PIN_PRORP-Zc3h12a-like cd18671
PIN domain of protein-only RNase P (PRORP), ribonuclease Zc3h12a, and related proteins; PRORPs ...
 573-652 4.74e-16

PIN domain of protein-only RNase P (PRORP), ribonuclease Zc3h12a, and related proteins; PRORPs catalyze the maturation of the 5' end of precursor tRNAs in eukaryotes. This family includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3, PRORP1 localizes to the chloroplast and the mitochondria, and PRORP2 and PRORP3 localize to the nucleus. Zc3h12a (zinc finger CCCH-type containing 12A, also known as MCPIP1/MCP induced protein 1 and Regnase-1) is a critical regulator of inflammatory response, with additional roles in defense against viruses and various stresses, cellular differentiation, and apoptosis. This PIN_PRORP-Zc3h12a-like family also includes Caenorhabditis elegans REGE-1 (REGnasE-1), which also functions as a cytoplasmic endonuclease. Additionally, it includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4, as well as N4BP1 (NEDD4-binding partner-1), NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350238  Cd Length: 126  Bit Score: 74.98  E-value: 4.74e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 573 AVVDGANVGLFSHKH--ISLSKINIVADVIRQRFQSRKLPLIVVHNRHLTGERMQKPSNRKLVEKWKLSNAIYATPTGSN 650
Cdd:cd18671     1 AVIDGANVGLSHQNKesFSCRQLLLAVNWFLERSHNNTDPLVFLHKWRVEQPRPVPPTDRHLLEEWEKKGILYATPPGSN 80


                  ..
gi 1443061532 651 DD 652
Cdd:cd18671    81 DD 82
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 354-451 2.05e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 47.95  E-value: 2.05e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532  354 SALTAVARMAmsmGNGDMAFDVVKQMKDQGIAPKLRSYGPALTAFCNSGNVEKAFEVEAHMLESGVRPEEPELETLLKAS 433
Cdd:PLN03218   653 SALVDVAGHA---GDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITAL 729

                           90
                   ....*....|....*...
gi 1443061532  434 VAAQQGDKVYYLLHKFRT 451
Cdd:PLN03218   730 CEGNQLPKALEVLSEMKR 747
PBP1_ABC_ligand_binding-like cd06338
type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type ...
 308-398 2.74e-03

type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT); however, their ligand specificity has not been determined experimentally.


Pssm-ID: 380561 [Multi-domain]  Cd Length: 347  Bit Score: 40.64  E-value: 2.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 308 LFASDDgtekPSRIPVSDELREYARTRGFEIfekmrSEEEKVPMNESALTAVARMAMSM--------GNGDMAFDVVKQM 379
Cdd:cd06338   146 IVYEDD----PFGKEVAEGAREAAKKAGLEV-----VYDESYPPGTTDFSPLLTKVKAAnpdillvgGYPPDAITLVRQM 216

                          90       100
                  ....*....|....*....|.
gi 1443061532 380 KDQGIAPKLR--SYGPALTAF 398
Cdd:cd06338   217 KELGYNPKAFflTVGPAFPAF 237
 
Name Accession Description Interval E-value
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 205-474 1.42e-76

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 243.84  E-value: 1.42e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 205 EVKLRVELDMCSKRGDVIGAINLYDSAVKEGIKMGQHHYSVLLYLCSSAALGFvqpaksgnagsgiasigqlhssstqsv 284
Cdd:pfam17177  11 ESELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADAT--------------------------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 285 gnlegddvqseghsedqegnktdlfasddgtekpsripvsDELREYARTRGFEIFEKMRSEeeKVPMNESALTAVARMAM 364
Cdd:pfam17177  64 ----------------------------------------DLKPQLAADRGFEVFEAMKAQ--GVSPNEATYTAVARLAA 101

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 365 SMGNGDMAFDVVKQMKDQGIAPKLRSYGPALTAFCNSGNVEKAFEVEAHMLESGVRPEEPELETLLKASVAAQQGDKVYY 444
Cdd:pfam17177 102 AKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYA 181

                         250       260       270
                  ....*....|....*....|....*....|
gi 1443061532 445 LLHKFRTTVRQASSTTAKLLEDWFQSPTAS 474
Cdd:pfam17177 182 YLHRLRDAVRQVSESTAGVLEEWFRSEAAA 211
PRORP pfam16953
Protein-only RNase P; PRORPs (protein-only RNase P) are a class of RNA processing enzymes that ...
 515-652 7.46e-47

Protein-only RNase P; PRORPs (protein-only RNase P) are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. Arabidopsis thaliana contains PRORP enzymes (PRORP1, PRORP2 and PRORP3) where PRORP1 localizes to mitochondria as well as chloroplasts, while PRORP2 and PRORP3 are found in the nucleus. In humans and most other metazoans, mt-RNase P is composed of three protein subunits (mitochondrial RNase P proteins 1-3; MRPP1-3), homologs to the Arabidopsis thaliana PRORP1-3. This domain corresponds to the metallonuclease domain of PRORPs. PRORP1 has 22% sequence identity to the human homolog MRPP3. PRORP1 crystal structure shows a V-shaped tripartite structure with a C-terminal metallonuclease domain of the NYN (N4BL1, YacP-like nuclease) family, with a typical and functional two-metal-ion catalytic site that has conserved aspartate residues.


Pssm-ID: 465320  Cd Length: 242  Bit Score: 165.60  E-value: 7.46e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 515 IDRNGACLACGEKLTIIDLDPKETEDFATLVAKLAIKRERR------SNFDNFQKWLEKHGPFDAVVDGANV-GLFSHKH 587
Cdd:pfam16953   1 IDKSGKCSSCGEKLESIDLSPEETENLAESVLRLVIIREDVfrkttpQEFNRFQKFLERTGPFDAVIDGLNVaGLFGQKR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1443061532 588 ISLSKINIVADVIRQrFQSRKLPLIVVHNRHLTGERMQKpsNRKLVEKWKLSNAIYATPTGSNDD 652
Cdd:pfam16953  81 FSIQQANNVVNVVRQ-LAPQKLRLLVLGRKHMLGGPSNW--NKALMEKWQNAAALFFTPNGSNDD 142
PIN_PRORP-Zc3h12a-like cd18671
PIN domain of protein-only RNase P (PRORP), ribonuclease Zc3h12a, and related proteins; PRORPs ...
 573-652 4.74e-16

PIN domain of protein-only RNase P (PRORP), ribonuclease Zc3h12a, and related proteins; PRORPs catalyze the maturation of the 5' end of precursor tRNAs in eukaryotes. This family includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3, PRORP1 localizes to the chloroplast and the mitochondria, and PRORP2 and PRORP3 localize to the nucleus. Zc3h12a (zinc finger CCCH-type containing 12A, also known as MCPIP1/MCP induced protein 1 and Regnase-1) is a critical regulator of inflammatory response, with additional roles in defense against viruses and various stresses, cellular differentiation, and apoptosis. This PIN_PRORP-Zc3h12a-like family also includes Caenorhabditis elegans REGE-1 (REGnasE-1), which also functions as a cytoplasmic endonuclease. Additionally, it includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4, as well as N4BP1 (NEDD4-binding partner-1), NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350238  Cd Length: 126  Bit Score: 74.98  E-value: 4.74e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 573 AVVDGANVGLFSHKH--ISLSKINIVADVIRQRFQSRKLPLIVVHNRHLTGERMQKPSNRKLVEKWKLSNAIYATPTGSN 650
Cdd:cd18671     1 AVIDGANVGLSHQNKesFSCRQLLLAVNWFLERSHNNTDPLVFLHKWRVEQPRPVPPTDRHLLEEWEKKGILYATPPGSN 80


                  ..
gi 1443061532 651 DD 652
Cdd:cd18671    81 DD 82
PIN_PRORP cd18718
PIN domain of protein-only RNase P (PRORP) and related proteins; PRORPs catalyze the ...
 573-662 1.15e-14

PIN domain of protein-only RNase P (PRORP) and related proteins; PRORPs catalyze the maturation of the 5' end of precursor tRNAs in eukaryotes. This family includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3, PRORP1 localizes to the chloroplast and the mitochondria, and PRORP2 and PRORP3 localize to the nucleus. This subfamily belongs to the PRORP-Zc3h12a-like PIN family which in addition includes Zc3h12a (also known as MCPIP1/MCP induced protein 1 and Regnase-1), Caenorhabditis elegans REGE-1 (REGnasE-1), Zc3h12b-d (also known as Regnase-2-4), N4BP1, and NYNRIN (also known as CGIN1). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350285  Cd Length: 124  Bit Score: 70.68  E-value: 1.15e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 573 AVVDGANVGLFSHKHISLSKINIVADVIRQRFQSRKLPLIVVHNRHLTGERMqKPSNRKLVEKwklSNAIYATPTGSNDD 652
Cdd:cd18718     1 VVIDGLNVAYYGQNFPGGFNAQQLLAVVEHLQKQNKKVLVLGRKHMLKWSRW-SPSAMKLIEK---NASLFFTPNGSNDD 76

                          90
                  ....*....|....*...
gi 1443061532 653 --------CSGTGCMLLS 662
Cdd:cd18718    77 pfwlyaalKSGPKTLFVS 94
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 354-451 2.05e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 47.95  E-value: 2.05e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532  354 SALTAVARMAmsmGNGDMAFDVVKQMKDQGIAPKLRSYGPALTAFCNSGNVEKAFEVEAHMLESGVRPEEPELETLLKAS 433
Cdd:PLN03218   653 SALVDVAGHA---GDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITAL 729

                           90
                   ....*....|....*...
gi 1443061532  434 VAAQQGDKVYYLLHKFRT 451
Cdd:PLN03218   730 CEGNQLPKALEVLSEMKR 747
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 331-451 3.47e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 44.10  E-value: 3.47e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532  331 ARTRGFEIFEKMRSEEEKVPMNESALTAVARMAMSMGNGDMAFDVVKQMKDQGIAPKLRSYGPALTAFCNSGNVEKAFEV 410
Cdd:PLN03218   557 AVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSI 636

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1443061532  411 EAHMLESGVRPEEPELETLLKASVAAQQGDKVYYLLHKFRT 451
Cdd:PLN03218   637 YDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARK 677
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 375-421 5.35e-04

Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 38.49  E-value: 5.35e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1443061532 375 VVKQMKDQGIAPKLRSYGPALTAFCNSGNVEKAFEVEAHMLESGVRP 421
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKP 48
PIN_SF cd09852
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
 574-654 1.16e-03

PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. The PIN domain superfamily includes: the FEN-like PIN domain family such as the PIN domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. It also includes the Mut7-C PIN domain family, which is not represented here as it is a shortened version of the PIN fold and lacks a core strand and helix (H3 and S3). The Mut7-C PIN domain family includes the C-terminus of Caenorhabditis elegans exonuclease Mut-7.


Pssm-ID: 350203  Cd Length: 114  Bit Score: 39.15  E-value: 1.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 574 VVDGANVGL-FSHKHISLSKINIVADVIrQRFQSRKLPLIVVHNRHLTGERMQKPSNRKLVEKWKLSNAIYATPTGSNDD 652
Cdd:cd09852     1 LVDGSNMIYtCREAVRTYRLNFDMAQRQ-YVAKEGVSPIVVFDASPVQLKVKVTKNDRKQLQFHGVGFAV*LTPPISDAD 79


                  ..
gi 1443061532 653 CS 654
Cdd:cd09852    80 VG 81
PBP1_ABC_ligand_binding-like cd06338
type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type ...
 308-398 2.74e-03

type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT); however, their ligand specificity has not been determined experimentally.


Pssm-ID: 380561 [Multi-domain]  Cd Length: 347  Bit Score: 40.64  E-value: 2.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443061532 308 LFASDDgtekPSRIPVSDELREYARTRGFEIfekmrSEEEKVPMNESALTAVARMAMSM--------GNGDMAFDVVKQM 379
Cdd:cd06338   146 IVYEDD----PFGKEVAEGAREAAKKAGLEV-----VYDESYPPGTTDFSPLLTKVKAAnpdillvgGYPPDAITLVRQM 216

                          90       100
                  ....*....|....*....|.
gi 1443061532 380 KDQGIAPKLR--SYGPALTAF 398
Cdd:cd06338   217 KELGYNPKAFflTVGPAFPAF 237
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH