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Conserved domains on  [gi|375493513|ref|NP_001243607|]
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mitochondrial ribonuclease P catalytic subunit isoform 2 [Homo sapiens]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 11246529)

pentatricopeptide repeat (PPR)-containing protein may form anti-parallel alpha helices and bind single-stranded RNA in a sequence-specific and modular manner

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 ...
 328-562 2.86e-140

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: 405.58  E-value: 2.86e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513  328 ESGQCSGCGKTIESIQLSPEEYECLKGKIMRDVIDGGDQYRKTTPQELKRFENFIKSRPPFDVVIDGLNVAKMFPKVRES 407
Cdd:pfam16953   3 KSGKCSSCGEKLESIDLSPEETENLAESVLRLVIIREDVFRKTTPQEFNRFQKFLERTGPFDAVIDGLNVAGLFGQKRFS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513  408 ----QLLLNVVSQLAKRNLRLLVLGRKHMLRRSSQWSRDEMEEVQKQASCFFADDISEDDPFLLYATLHSGNHCRFITRD 483
Cdd:pfam16953  83 iqqaNNVVNVVRQLAPQKLRLLVLGRKHMLGGPSNWNKALMEKWQNAAALFFTPNGSNDDPFLLYATLRSGNKCLFVTRD 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513  484 LMRDHKACLPDAKTQRLFFKWQQGHQLAIVNRFPGSKLTFQRILSYDTVVQTTGD-SWHIPYDEDLVERCSCEVPTKWLC 562
Cdd:pfam16953 163 LMRDHKFCLLGNDLKRFFPRWQQGHQLVLLSFSPGGGITFHMPPPYSTVIQESEDgTWHIPYDEDYVERDSYEVPRKWLC 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 ...
 328-562 2.86e-140

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: 405.58  E-value: 2.86e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513  328 ESGQCSGCGKTIESIQLSPEEYECLKGKIMRDVIDGGDQYRKTTPQELKRFENFIKSRPPFDVVIDGLNVAKMFPKVRES 407
Cdd:pfam16953   3 KSGKCSSCGEKLESIDLSPEETENLAESVLRLVIIREDVFRKTTPQEFNRFQKFLERTGPFDAVIDGLNVAGLFGQKRFS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513  408 ----QLLLNVVSQLAKRNLRLLVLGRKHMLRRSSQWSRDEMEEVQKQASCFFADDISEDDPFLLYATLHSGNHCRFITRD 483
Cdd:pfam16953  83 iqqaNNVVNVVRQLAPQKLRLLVLGRKHMLGGPSNWNKALMEKWQNAAALFFTPNGSNDDPFLLYATLRSGNKCLFVTRD 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513  484 LMRDHKACLPDAKTQRLFFKWQQGHQLAIVNRFPGSKLTFQRILSYDTVVQTTGD-SWHIPYDEDLVERCSCEVPTKWLC 562
Cdd:pfam16953 163 LMRDHKFCLLGNDLKRFFPRWQQGHQLVLLSFSPGGGITFHMPPPYSTVIQESEDgTWHIPYDEDYVERDSYEVPRKWLC 242
PIN_PRORP cd18718
PIN domain of protein-only RNase P (PRORP) and related proteins; PRORPs catalyze the ...
 390-512 1.80e-57

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: 188.16  E-value: 1.80e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513 390 VVIDGLNVAKM---FPKVRESQLLLNVVSQLAKRNLRLLVLGRKHMLRRSSqWSRDEMEEVQKQASCFFADDISEDDPFL 466
Cdd:cd18718    1 VVIDGLNVAYYgqnFPGGFNAQQLLAVVEHLQKQNKKVLVLGRKHMLKWSR-WSPSAMKLIEKNASLFFTPNGSNDDPFW 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 375493513 467 LYATLHSGNHCRFITRDLMRDHKACLPDaKTQRLFFKWQQGHQLAI 512
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 ...
 328-562 2.86e-140

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: 405.58  E-value: 2.86e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513  328 ESGQCSGCGKTIESIQLSPEEYECLKGKIMRDVIDGGDQYRKTTPQELKRFENFIKSRPPFDVVIDGLNVAKMFPKVRES 407
Cdd:pfam16953   3 KSGKCSSCGEKLESIDLSPEETENLAESVLRLVIIREDVFRKTTPQEFNRFQKFLERTGPFDAVIDGLNVAGLFGQKRFS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513  408 ----QLLLNVVSQLAKRNLRLLVLGRKHMLRRSSQWSRDEMEEVQKQASCFFADDISEDDPFLLYATLHSGNHCRFITRD 483
Cdd:pfam16953  83 iqqaNNVVNVVRQLAPQKLRLLVLGRKHMLGGPSNWNKALMEKWQNAAALFFTPNGSNDDPFLLYATLRSGNKCLFVTRD 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513  484 LMRDHKACLPDAKTQRLFFKWQQGHQLAIVNRFPGSKLTFQRILSYDTVVQTTGD-SWHIPYDEDLVERCSCEVPTKWLC 562
Cdd:pfam16953 163 LMRDHKFCLLGNDLKRFFPRWQQGHQLVLLSFSPGGGITFHMPPPYSTVIQESEDgTWHIPYDEDYVERDSYEVPRKWLC 242
PIN_PRORP cd18718
PIN domain of protein-only RNase P (PRORP) and related proteins; PRORPs catalyze the ...
 390-512 1.80e-57

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: 188.16  E-value: 1.80e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513 390 VVIDGLNVAKM---FPKVRESQLLLNVVSQLAKRNLRLLVLGRKHMLRRSSqWSRDEMEEVQKQASCFFADDISEDDPFL 466
Cdd:cd18718    1 VVIDGLNVAYYgqnFPGGFNAQQLLAVVEHLQKQNKKVLVLGRKHMLKWSR-WSPSAMKLIEKNASLFFTPNGSNDDPFW 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 375493513 467 LYATLHSGNHCRFITRDLMRDHKACLPDaKTQRLFFKWQQGHQLAI 512
Cdd:cd18718   80 LYAALKSGPKTLFVSNDLMRDHKFQLLD-ELQRLFKKWQERHQVRF 124
PIN_PRORP-Zc3h12a-like cd18671
PIN domain of protein-only RNase P (PRORP), ribonuclease Zc3h12a, and related proteins; PRORPs ...
 390-512 1.81e-05

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: 44.55  E-value: 1.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375493513 390 VVIDGLNVAkMFPKVRES---QLLLNVVSQLAKRN------LRLLVLGRKHMLRRSSQWSRDEMEEVQKQASCFFADDIS 460
Cdd:cd18671    1 AVIDGANVG-LSHQNKESfscRQLLLAVNWFLERShnntdpLVFLHKWRVEQPRPVPPTDRHLLEEWEKKGILYATPPGS 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 375493513 461 EDDPFLLYATLHSgnHCRFITRDLMRDHkacLPDAKTQRLFFKWQQGHQLAI 512
Cdd:cd18671   80 NDDWYWLYAAYES--KCLLVTNDEMRDH---QFELLGRQFFKRWKEEHQVRY 126
 
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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