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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2007383207  12 GSQNPEAKFQFELNTCSKAKDLRGAISLYDDAVSNNTRLNQHHFNALLYLCSNS-VADPSLKSTALDYGFRAFCHMSALA 90
Cdd:pfam17177   6 GKQTPESELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAaDATDLKPQLAADRGFEVFEAMKAQG 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2007383207  91 VLPNEATVTAVARLAAAKGDAGYAFDLVKSMGKNynNALPRLRTYDPALFCFCEMLDADKAYEVEEHMSGVGVSLEEAEV 170
Cdd:pfam17177  86 VSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAA--GVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPEL 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2007383207 171 AALLKVSARCGRADKVYEYLHKLRSSVRCVSESSAVVIEEWFRGSKSSE 219
Cdd:pfam17177 164 AALLKVSAKAGRADKVYAYLHRLRDAVRQVSESTAGVLEEWFRSEAAAE 212

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2007383207  12 GSQNPEAKFQFELNTCSKAKDLRGAISLYDDAVSNNTRLNQHHFNALLYLCSNS-VADPSLKSTALDYGFRAFCHMSALA 90
Cdd:pfam17177   6 GKQTPESELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAaDATDLKPQLAADRGFEVFEAMKAQG 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2007383207  91 VLPNEATVTAVARLAAAKGDAGYAFDLVKSMGKNynNALPRLRTYDPALFCFCEMLDADKAYEVEEHMSGVGVSLEEAEV 170
Cdd:pfam17177  86 VSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAA--GVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPEL 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2007383207 171 AALLKVSARCGRADKVYEYLHKLRSSVRCVSESSAVVIEEWFRGSKSSE 219
Cdd:pfam17177 164 AALLKVSAKAGRADKVYAYLHRLRDAVRQVSESTAGVLEEWFRSEAAAE 212

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2007383207 317 AIVDGANIGLYQQNFadGGFSISQLDDVVKELYNRSG-KKWPLVVLHNKRLRGLM-ENPSSRRLVEEWMNNGALYTTPNG 394
Cdd:cd18671     1 AVIDGANVGLSHQNK--ESFSCRQLLLAVNWFLERSHnNTDPLVFLHKWRVEQPRpVPPTDRHLLEEWEKKGILYATPPG 78

                          90
                  ....*....|....*....
gi 2007383207 395 SNDDWYWLFAAVKLRCLLV 413
Cdd:cd18671    79 SNDDWYWLYAAYESKCLLV 97

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2007383207  12 GSQNPEAKFQFELNTCSKAKDLRGAISLYDDAVSNNTRLNQHHFNALLYLCSNS-VADPSLKSTALDYGFRAFCHMSALA 90
Cdd:pfam17177   6 GKQTPESELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAaDATDLKPQLAADRGFEVFEAMKAQG 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2007383207  91 VLPNEATVTAVARLAAAKGDAGYAFDLVKSMGKNynNALPRLRTYDPALFCFCEMLDADKAYEVEEHMSGVGVSLEEAEV 170
Cdd:pfam17177  86 VSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAA--GVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPEL 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2007383207 171 AALLKVSARCGRADKVYEYLHKLRSSVRCVSESSAVVIEEWFRGSKSSE 219
Cdd:pfam17177 164 AALLKVSAKAGRADKVYAYLHRLRDAVRQVSESTAGVLEEWFRSEAAAE 212

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2007383207 317 AIVDGANIGLYQQNFadGGFSISQLDDVVKELYNRSG-KKWPLVVLHNKRLRGLM-ENPSSRRLVEEWMNNGALYTTPNG 394
Cdd:cd18671     1 AVIDGANVGLSHQNK--ESFSCRQLLLAVNWFLERSHnNTDPLVFLHKWRVEQPRpVPPTDRHLLEEWEKKGILYATPPG 78

                          90
                  ....*....|....*....
gi 2007383207 395 SNDDWYWLFAAVKLRCLLV 413
Cdd:cd18671    79 SNDDWYWLYAAYESKCLLV 97

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2007383207 318 IVDGANIGLYQQNFADGGFSISQLDDvvKELYNRSGKKwPLVVLHNKRLRGLMEN-PSSRRLVEEWMNNGALYTTPNGSN 396
Cdd:cd09852     1 LVDGSNMIYTCREAVRTYRLNFDMAQ--RQYVAKEGVS-PIVVFDASPVQLKVKVtKNDRKQLQFHGVGFAV*LTPPISD 77

                          90
                  ....*....|....*....
gi 2007383207 397 DDWYWLFAAVKL-RCLLVH 414
Cdd:cd09852    78 ADVGIAALAIAIdRVALAT 96