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Conserved domains on  [gi|227908787|ref|NP_079649|]
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mitochondrial ribonuclease P catalytic subunit precursor [Mus musculus]

Protein Classification

PIN_PRORP domain-containing protein( domain architecture ID 11246529)

PIN_PRORP domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRORP pfam16953
Protein-only RNase P; PRORPs (protein-only RNase P) are a class of RNA processing enzymes that ...
 339-575 1.29e-129

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: 379.39  E-value: 1.29e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787  339 IQKSGQCSGCGRTIEPIHLSPEEYEFLKEKIMRDVIDGGDQYKKTTPQELKRFESFVNSCPPFDIVIDGLNVAKMFPKGR 418
Cdd:pfam16953   1 IDKSGKCSSCGEKLESIDLSPEETENLAESVLRLVIIREDVFRKTTPQEFNRFQKFLERTGPFDAVIDGLNVAGLFGQKR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787  419 ES----QNLLGVVSQLAQQNLQLLVLGRKHMLRPSSQWRKEEMEQVRKQAHCFFADNISEDDPFLLYATLNSGNHCKFIT 494
Cdd:pfam16953  81 FSiqqaNNVVNVVRQLAPQKLRLLVLGRKHMLGGPSNWNKALMEKWQNAAALFFTPNGSNDDPFLLYATLRSGNKCLFVT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787  495 KDLLRDHKACLPDARTQRLFFKWQQGHQLAIMKGFQKSKLTFQHILSYDTVVQRTGD-SWHIPYDEDLVQRSSCEVPTKW 573
Cdd:pfam16953 161 RDLMRDHKFCLLGNDLKRFFPRWQQGHQLVLLSFSPGGGITFHMPPPYSTVIQESEDgTWHIPYDEDYVERDSYEVPRKW 240


                  ..
gi 227908787  574 LC 575
Cdd:pfam16953 241 LC 242
 
Name Accession Description Interval E-value
PRORP pfam16953
Protein-only RNase P; PRORPs (protein-only RNase P) are a class of RNA processing enzymes that ...
 339-575 1.29e-129

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: 379.39  E-value: 1.29e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787  339 IQKSGQCSGCGRTIEPIHLSPEEYEFLKEKIMRDVIDGGDQYKKTTPQELKRFESFVNSCPPFDIVIDGLNVAKMFPKGR 418
Cdd:pfam16953   1 IDKSGKCSSCGEKLESIDLSPEETENLAESVLRLVIIREDVFRKTTPQEFNRFQKFLERTGPFDAVIDGLNVAGLFGQKR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787  419 ES----QNLLGVVSQLAQQNLQLLVLGRKHMLRPSSQWRKEEMEQVRKQAHCFFADNISEDDPFLLYATLNSGNHCKFIT 494
Cdd:pfam16953  81 FSiqqaNNVVNVVRQLAPQKLRLLVLGRKHMLGGPSNWNKALMEKWQNAAALFFTPNGSNDDPFLLYATLRSGNKCLFVT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787  495 KDLLRDHKACLPDARTQRLFFKWQQGHQLAIMKGFQKSKLTFQHILSYDTVVQRTGD-SWHIPYDEDLVQRSSCEVPTKW 573
Cdd:pfam16953 161 RDLMRDHKFCLLGNDLKRFFPRWQQGHQLVLLSFSPGGGITFHMPPPYSTVIQESEDgTWHIPYDEDYVERDSYEVPRKW 240


                  ..
gi 227908787  574 LC 575
Cdd:pfam16953 241 LC 242
PIN_PRORP cd18718
PIN domain of protein-only RNase P (PRORP) and related proteins; PRORPs catalyze the ...
 403-525 3.20e-46

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: 158.50  E-value: 3.20e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787 403 IVIDGLNVAKM---FPKGRESQNLLGVVSQLAQQNLQLLVLGRKHMLRPSSqWRKEEMEQVRKQAHCFFADNISEDDPFL 479
Cdd:cd18718    1 VVIDGLNVAYYgqnFPGGFNAQQLLAVVEHLQKQNKKVLVLGRKHMLKWSR-WSPSAMKLIEKNASLFFTPNGSNDDPFW 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 227908787 480 LYATLNSGNHCKFITKDLLRDHKACLPDaRTQRLFFKWQQGHQLAI 525
Cdd:cd18718   80 LYAALKSGPKTLFVSNDLMRDHKFQLLD-ELQRLFKKWQERHQVRF 124
 
Name Accession Description Interval E-value
PRORP pfam16953
Protein-only RNase P; PRORPs (protein-only RNase P) are a class of RNA processing enzymes that ...
 339-575 1.29e-129

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: 379.39  E-value: 1.29e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787  339 IQKSGQCSGCGRTIEPIHLSPEEYEFLKEKIMRDVIDGGDQYKKTTPQELKRFESFVNSCPPFDIVIDGLNVAKMFPKGR 418
Cdd:pfam16953   1 IDKSGKCSSCGEKLESIDLSPEETENLAESVLRLVIIREDVFRKTTPQEFNRFQKFLERTGPFDAVIDGLNVAGLFGQKR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787  419 ES----QNLLGVVSQLAQQNLQLLVLGRKHMLRPSSQWRKEEMEQVRKQAHCFFADNISEDDPFLLYATLNSGNHCKFIT 494
Cdd:pfam16953  81 FSiqqaNNVVNVVRQLAPQKLRLLVLGRKHMLGGPSNWNKALMEKWQNAAALFFTPNGSNDDPFLLYATLRSGNKCLFVT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787  495 KDLLRDHKACLPDARTQRLFFKWQQGHQLAIMKGFQKSKLTFQHILSYDTVVQRTGD-SWHIPYDEDLVQRSSCEVPTKW 573
Cdd:pfam16953 161 RDLMRDHKFCLLGNDLKRFFPRWQQGHQLVLLSFSPGGGITFHMPPPYSTVIQESEDgTWHIPYDEDYVERDSYEVPRKW 240


                  ..
gi 227908787  574 LC 575
Cdd:pfam16953 241 LC 242
PIN_PRORP cd18718
PIN domain of protein-only RNase P (PRORP) and related proteins; PRORPs catalyze the ...
 403-525 3.20e-46

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: 158.50  E-value: 3.20e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227908787 403 IVIDGLNVAKM---FPKGRESQNLLGVVSQLAQQNLQLLVLGRKHMLRPSSqWRKEEMEQVRKQAHCFFADNISEDDPFL 479
Cdd:cd18718    1 VVIDGLNVAYYgqnFPGGFNAQQLLAVVEHLQKQNKKVLVLGRKHMLKWSR-WSPSAMKLIEKNASLFFTPNGSNDDPFW 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 227908787 480 LYATLNSGNHCKFITKDLLRDHKACLPDaRTQRLFFKWQQGHQLAI 525
Cdd:cd18718   80 LYAALKSGPKTLFVSNDLMRDHKFQLLD-ELQRLFKKWQERHQVRF 124
 
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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