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 119627753 138 VVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEKKKILVFTPSRRVG 217
Cdd:cd18729    1 IVIDGSNVAMSHGNKEVFSCRGIQLAVDWFRERGHRDITVFVPSWRKEQPRPDAPITDQEILRELEKEKILVFTPSRRVG 80

                         90       100
                 ....*....|....*....|....*
gi 119627753 218 GKRVVCYDDRFIVKLAYESDGIVAS 242
Cdd:cd18729   81 GKRVVCYDDRFILKLAYESDGIVVS 105

PRORP-like PIN domain of ribonuclease Zc3h12a and related proteins; 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 subfamily also includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4. It belongs to the Zc3h12a-N4BP1-like PIN subfamily of the PRORP-Zc3h12a-like PIN family, the latter of which additionally includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. 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 119627753 138 VVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEKKKILVFTPSRRVG 217
Cdd:cd18729    1 IVIDGSNVAMSHGNKEVFSCRGIQLAVDWFRERGHRDITVFVPSWRKEQPRPDAPITDQEILRELEKEKILVFTPSRRVG 80

                         90       100
                 ....*....|....*....|....*
gi 119627753 218 GKRVVCYDDRFIVKLAYESDGIVAS 242
Cdd:cd18729   81 GKRVVCYDDRFILKLAYESDGIVVS 105

UBA-like domain; This entry represents a UBA-like domain found at the N-terminus of ribonuclease ZC3 proteins.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 119627753   49 QMKVDFFRKLGYSSTEIHSVLQKLGVQADTNTVLGELVKHG 89
Cdd:pfam18039   2 KERVDFALKLGYSEEQVQAVLQKLGPEADTDKVLGELIKLG 42

PRORP-like PIN domain of ribonuclease Zc3h12a and related proteins; 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 subfamily also includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4. It belongs to the Zc3h12a-N4BP1-like PIN subfamily of the PRORP-Zc3h12a-like PIN family, the latter of which additionally includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. 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 119627753 138 VVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEKKKILVFTPSRRVG 217
Cdd:cd18729    1 IVIDGSNVAMSHGNKEVFSCRGIQLAVDWFRERGHRDITVFVPSWRKEQPRPDAPITDQEILRELEKEKILVFTPSRRVG 80

                         90       100
                 ....*....|....*....|....*
gi 119627753 218 GKRVVCYDDRFIVKLAYESDGIVAS 242
Cdd:cd18729   81 GKRVVCYDDRFILKLAYESDGIVVS 105

Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes. It has been suggested that this domain belongs to the PIN domain superfamily. This domain has also been identified as part of the NYN domain family.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119627753  134 DLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRpdvPITDQHILRELEKKKILVFTPS 213
Cdd:pfam11977   1 GLRPIVIDGSNVAMSHGRQKKFSVRGLAIAVDYFVKRGHEEITVFVPQWRKEADE---KITDQHELLELERLGLIVFTPS 77

                          90       100
                  ....*....|....*....|....*....
gi 119627753  214 RRVGGKRVVCYDDRFIVKLAYESDGIVAS 242
Cdd:pfam11977  78 RTLDGKRIVSYDDRFILKLAEETDGVIVS 106

PRORP-like PIN domain of NEDD4 binding protein 1 and related proteins; NEDD4-binding partner-1 (N4BP1) interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. This subfamily additionally includes 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. This subfamily belongs to the Zc3h12a-N4BP1-like PIN subfamily of the PRORP-Zc3h12a-like PIN family, the latter of which additionally includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. 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 119627753 138 VVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKeqpRPDVPITDQHILRELEKKKILVFTPSRRVG 217
Cdd:cd18728    1 IVIDGSNVAMVHGLQHFFSCRGIAIAVEYFWKRGHRNITVFVPQWRT---KRDPNVTEQHFLTQLQELGILSLTPSRMVL 77

                         90       100
                 ....*....|....*....|....*
gi 119627753 218 GKRVVCYDDRFIVKLAYESDGIVAS 242
Cdd:cd18728   78 GKRIASHDDRFLLHLAEKTGGIIVT 102