GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896092863 113 CIYRI-YAGNE-IYIGLTYDT-KQRFSSHRKK-----TTQVIDLIERHGIENVKFEQLTEYMNQELAQIAEKEHIEYYRN 184
Cdd:cd10443     2 VIYKItNPINGkVYIGQTTRTlEERLKQHKKAasagpKKDFYNAIRKYGWDNFTIEILDEGESKEELNELEIEYIAEYNS 81

                  ....*....
gi 1896092863 185 NGWIILNRS 193
Cdd:cd10443    82 NGPNGYNLT 90

GIY-YIG domain of uncharacterized hypothetical protein found in phycodnavirus PBCV-1 DNA virus, T. thermophila Tlr element eoncoding protein Tlr8p, and similar proteins found in bacteria; The family includes a group of diverse uncharacterized hypothetical proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI. Similar to I-TevI, family members from phycodnavirus PBCV-1 DNA virus have nuclease-associated modular DNA-binding domains (NUMODs) and a helix-turn-helix (HTH) domain C-terminally fused to the GIY-YIG domain, which suggests that these PBCV-1 acquired the I-TevI-like homing endonucleases from phages by horizontal gene transfer. This family also includes proteins that appear to connect homing endonucleases with Penelope elements, such as Tetrahymena thermophila Tlr element encoding protein Tlr8p that possess additional N-terminal and central structural regions, followed by a putative superfamily 1 helicase domain and I-TevI-like GIY-YIG domain, but lacks the NUMOD domains and HTH domain. It is suggested that the Tlr8p element could have acquired its GIY-YIG domain w ithin the nucleus of the ciliate cell infected by the Phycodnavirus. Some family members only contain a standalone GIY-YIG domain and their biological functions are unclear.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896092863 113 CIYRI-YAGNE-IYIGLTYDT-KQRFSSHRKK-----TTQVIDLIERHGIENVKFEQLTEYMNQELAQIAEKEHIEYYRN 184
Cdd:cd10443     2 VIYKItNPINGkVYIGQTTRTlEERLKQHKKAasagpKKDFYNAIRKYGWDNFTIEILDEGESKEELNELEIEYIAEYNS 81

                  ....*....
gi 1896092863 185 NGWIILNRS 193
Cdd:cd10443    82 NGPNGYNLT 90

GIY-YIG domain of uncharacterized hypothetical protein found in phycodnavirus PBCV-1 DNA virus, T. thermophila Tlr element eoncoding protein Tlr8p, and similar proteins found in bacteria; The family includes a group of diverse uncharacterized hypothetical proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI. Similar to I-TevI, family members from phycodnavirus PBCV-1 DNA virus have nuclease-associated modular DNA-binding domains (NUMODs) and a helix-turn-helix (HTH) domain C-terminally fused to the GIY-YIG domain, which suggests that these PBCV-1 acquired the I-TevI-like homing endonucleases from phages by horizontal gene transfer. This family also includes proteins that appear to connect homing endonucleases with Penelope elements, such as Tetrahymena thermophila Tlr element encoding protein Tlr8p that possess additional N-terminal and central structural regions, followed by a putative superfamily 1 helicase domain and I-TevI-like GIY-YIG domain, but lacks the NUMOD domains and HTH domain. It is suggested that the Tlr8p element could have acquired its GIY-YIG domain w ithin the nucleus of the ciliate cell infected by the Phycodnavirus. Some family members only contain a standalone GIY-YIG domain and their biological functions are unclear.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896092863 113 CIYRI-YAGNE-IYIGLTYDT-KQRFSSHRKK-----TTQVIDLIERHGIENVKFEQLTEYMNQELAQIAEKEHIEYYRN 184
Cdd:cd10443     2 VIYKItNPINGkVYIGQTTRTlEERLKQHKKAasagpKKDFYNAIRKYGWDNFTIEILDEGESKEELNELEIEYIAEYNS 81

                  ....*....
gi 1896092863 185 NGWIILNRS 193
Cdd:cd10443    82 NGPNGYNLT 90

GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896092863 113 CIYRIY--AGNEIYIGLTYDTKQRFSSH----RKKTTQvidlieRHGIENVKFEQLTEYMNQELAQIAEKEHIEYYRNNG 186
Cdd:pfam01541   3 GIYIIRnkDNKLLYVGSTKNLERRLNQHnagkGAKYTR------GKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPNK 76