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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102618198  12 CGIYCIRNTVNNKCYIGKSVNIYERMRCHINLLnKRSKNENLYFINAWHKYGRNCFEYTVLEDCvKDNDLLKERELYYIK 91
Cdd:cd10437     1 SGIYKITNLENGKIYIGSSKNILKRLSQHKRDL-KAGKHHNKKLQRDFNKYGEENFEFTILEEG-EEIEKLLELEQEYID 78

                          90
                  ....*....|...
gi 1102618198  92 FYntiDKKFGYNL 104
Cdd:cd10437    79 KY---KSEKGYNI 88

N-terminal catalytic domain of GIY-YIG intron endonuclease I-TevI, I-BmoI, I-BanI, I-BthII and similar proteins; I-TevI is a site-specific GIY-YIG homing endonuclease encoded within the group I intron of the thymidylate synthase gene (td) from Escherichia coli phage T4. It functions as an endonuclease that catalyzes the first step in intron homing by generating a double-strand break in the intronless td allele within a sequence designated the homing site. I-TevI recognizes its extensive 37 base pair DNA target in a site-specific, but sequence-tolerant manner. The cleavage site is located at 23 (upper strand) and 25 (lower strand) nucleotides upstream of the intron insertion site. A divalent cation, such as Mg2+, is required for the catalysis. I-TevI also acts as a repressor of its own transcription. It binds an operator that is located upstream of the I-TevI coding sequence and overlaps the T4 late promoter, which drives I-TevI expression from within the td intron. I-TevI binds the homing sites and the operator with the same affinity, but cleaves the homing site more efficiently than the operator. I-TevI consists of an N-terminal catalytic domain, containing the GIY-YIG motif, and a C-terminal DNA-binding domain that binds DNA as a monomer, joined by a flexible linker. The C-terminal domain includes three subdomains: a zinc finger, a minor-groove binding alpha-helix (NUMOD3, nuclease-associated modular domain 3), and a helix-turn-helix domain (HTH). The last two are responsible for DNA-binding. The zinc finger is part of the linker and not required for DNA-binding. It is implicated as a distance sensor to constrain the catalytic domain to cleave the homing site at a fixed position. None of other GIY-YIG endonucleases have been found to have the zinc finger motif. This family also includes a reduced activity isoschizomer of I-TevI, I-BmoI, which is encoded within the group I intron of the thymidylate synthase (TS) gene (thyA) from Bacillus mojavensis. I-BmoI catalyzes the first step in intron homing by generating a double-strand break in the intronless td allele within a sequence designated the homing site in the presence of a divalent cation cofactor, such as Mg2+. In the absence of Mg2+, I-Bmol only nicks one of the strands. Both I-BmoI and I-TevI bind a homologous stretch of TS-encoding DNA as monomers, but use different strategies to distinguish intronless from intron-containing substrates. I-TevI recognizes substrates at the level of DNA-binding. However, I-BmoI binds both intron-containing and intronless TS-encoding substrates, but efficiently cleaves only intronless substrate. Afterwards they cleave their respective intronless substrates in the same positions, and both require a critical G-C base pair adjacent to the top strand site for efficient cleavage. The C-terminal domain of I-BmoI has nuclease-associated modular DNA-binding domains (NUMODs), but lacks the zinc finger, which is different from that of I-TevI. Although the zinc finger implicated as a distance determination in I-TevI is absent, I-BmoI still possesses some cleavage distance discrimination. Besides I-TevI and I-BmoI, this family contains a putative GIY-YIG homing endonuclease, I-BanI, encoded within the self-splicing group I intron of nrdE gene from Bacillus anthracis. It contains two major domains, the N-terminal GIY-YIG domain and the C-terminal DNA-binding domain that consists of a minor-groove DNA binding alpha-helix motif and a helix-turn-helix (HTH) motif. I-BanI generates a double-strand break (DSB) in the intronless nrdE gene. The cleavage site is located at 5 and 7 nucleotides upstream of the intron insertion site, with 2-nucleotide 3' extensions. The recognition site is 35 to 40 base pairs and covers the cleavage site with a bias toward the downstream region including the (intervening sequence) IVS insertion site. Moreover, this family contains another putative GIY-YIG homing endonuclease, I-BthII, encoded within the self-splicing group I intron of nrdF gene from Bacillus thuringiensis ssp. pakistani. It contains a GIY-YIG motif that generates a double-strand break (DSB) in the intronless nrdF gene. The cleavage site is located at 7 and 9 nucleotides upstream of the intron insertion site, leaving 2-nucleotide 3' extensions. The recognition site is 27 to 29 base pairs with the DSB cleavage site at the 5'-end of the top strand, and with the intervening sequence (IVS) insertion site approximately in the middle of the recognition site.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102618198  12 CGIYCIRNTVNNKCYIGKSVNIYERMRCHINLLnKRSKNENLYFINAWHKYGRNCFEYTVLEDCvKDNDLLKERELYYIK 91
Cdd:cd10437     1 SGIYKITNLENGKIYIGSSKNILKRLSQHKRDL-KAGKHHNKKLQRDFNKYGEENFEFTILEEG-EEIEKLLELEQEYID 78

                          90
                  ....*....|...
gi 1102618198  92 FYntiDKKFGYNL 104
Cdd:cd10437    79 KY---KSEKGYNI 88

GIY-YIG type nucleases (URI domain);

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102618198   13 GIYCIRNTVNNKCYIGKSVNIYERMRCHINLLNKRSKnenlyFINAWHKYGRNcFEYTVLEDCvkdNDLLKERELYYIKF 92
Cdd:smart00465   3 GVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRL-----LIDALLKYGGN-FEFIILESF---DESALELEKYLIKE 73

                           90
                   ....*....|....
gi 1102618198   93 YntidkKFGYNLRM 106
Cdd:smart00465  74 Y-----KPKYNLLL 82

N-terminal catalytic domain of GIY-YIG intron endonuclease I-TevI, I-BmoI, I-BanI, I-BthII and similar proteins; I-TevI is a site-specific GIY-YIG homing endonuclease encoded within the group I intron of the thymidylate synthase gene (td) from Escherichia coli phage T4. It functions as an endonuclease that catalyzes the first step in intron homing by generating a double-strand break in the intronless td allele within a sequence designated the homing site. I-TevI recognizes its extensive 37 base pair DNA target in a site-specific, but sequence-tolerant manner. The cleavage site is located at 23 (upper strand) and 25 (lower strand) nucleotides upstream of the intron insertion site. A divalent cation, such as Mg2+, is required for the catalysis. I-TevI also acts as a repressor of its own transcription. It binds an operator that is located upstream of the I-TevI coding sequence and overlaps the T4 late promoter, which drives I-TevI expression from within the td intron. I-TevI binds the homing sites and the operator with the same affinity, but cleaves the homing site more efficiently than the operator. I-TevI consists of an N-terminal catalytic domain, containing the GIY-YIG motif, and a C-terminal DNA-binding domain that binds DNA as a monomer, joined by a flexible linker. The C-terminal domain includes three subdomains: a zinc finger, a minor-groove binding alpha-helix (NUMOD3, nuclease-associated modular domain 3), and a helix-turn-helix domain (HTH). The last two are responsible for DNA-binding. The zinc finger is part of the linker and not required for DNA-binding. It is implicated as a distance sensor to constrain the catalytic domain to cleave the homing site at a fixed position. None of other GIY-YIG endonucleases have been found to have the zinc finger motif. This family also includes a reduced activity isoschizomer of I-TevI, I-BmoI, which is encoded within the group I intron of the thymidylate synthase (TS) gene (thyA) from Bacillus mojavensis. I-BmoI catalyzes the first step in intron homing by generating a double-strand break in the intronless td allele within a sequence designated the homing site in the presence of a divalent cation cofactor, such as Mg2+. In the absence of Mg2+, I-Bmol only nicks one of the strands. Both I-BmoI and I-TevI bind a homologous stretch of TS-encoding DNA as monomers, but use different strategies to distinguish intronless from intron-containing substrates. I-TevI recognizes substrates at the level of DNA-binding. However, I-BmoI binds both intron-containing and intronless TS-encoding substrates, but efficiently cleaves only intronless substrate. Afterwards they cleave their respective intronless substrates in the same positions, and both require a critical G-C base pair adjacent to the top strand site for efficient cleavage. The C-terminal domain of I-BmoI has nuclease-associated modular DNA-binding domains (NUMODs), but lacks the zinc finger, which is different from that of I-TevI. Although the zinc finger implicated as a distance determination in I-TevI is absent, I-BmoI still possesses some cleavage distance discrimination. Besides I-TevI and I-BmoI, this family contains a putative GIY-YIG homing endonuclease, I-BanI, encoded within the self-splicing group I intron of nrdE gene from Bacillus anthracis. It contains two major domains, the N-terminal GIY-YIG domain and the C-terminal DNA-binding domain that consists of a minor-groove DNA binding alpha-helix motif and a helix-turn-helix (HTH) motif. I-BanI generates a double-strand break (DSB) in the intronless nrdE gene. The cleavage site is located at 5 and 7 nucleotides upstream of the intron insertion site, with 2-nucleotide 3' extensions. The recognition site is 35 to 40 base pairs and covers the cleavage site with a bias toward the downstream region including the (intervening sequence) IVS insertion site. Moreover, this family contains another putative GIY-YIG homing endonuclease, I-BthII, encoded within the self-splicing group I intron of nrdF gene from Bacillus thuringiensis ssp. pakistani. It contains a GIY-YIG motif that generates a double-strand break (DSB) in the intronless nrdF gene. The cleavage site is located at 7 and 9 nucleotides upstream of the intron insertion site, leaving 2-nucleotide 3' extensions. The recognition site is 27 to 29 base pairs with the DSB cleavage site at the 5'-end of the top strand, and with the intervening sequence (IVS) insertion site approximately in the middle of the recognition site.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102618198  12 CGIYCIRNTVNNKCYIGKSVNIYERMRCHINLLnKRSKNENLYFINAWHKYGRNCFEYTVLEDCvKDNDLLKERELYYIK 91
Cdd:cd10437     1 SGIYKITNLENGKIYIGSSKNILKRLSQHKRDL-KAGKHHNKKLQRDFNKYGEENFEFTILEEG-EEIEKLLELEQEYID 78

                          90
                  ....*....|...
gi 1102618198  92 FYntiDKKFGYNL 104
Cdd:cd10437    79 KY---KSEKGYNI 88

Catalytic GIY-YIG domain of putative intron-encoded endonuclease bI1 and similar proteins; The prototype of this family is a putative intron-encoded mitochondrial DNA endonuclease bI1 found in mitochondrion Ustilago maydis. This protein may arise from proteolytic cleavage of an in-frame translation of COB exon 1 plus intron 1, containing the bI1 open reading frame. It contains an N-terminal truncated non-functional cytochrome b region and a C-terminal intron-encoded endonuclease bI1 region. The bI1 region shows high sequence similarity to endonucleases of group I introns of fungi and phage and might be involved in intron homing. Many uncharacterized bI1 homologs existing in fungi and chlorophyta in this family do not contain the cytochrome b region, but have a standalone bI1-like region, which contains a GIY-YIG domain and a minor-groove binding alpha-helix nuclease-associated modular domain (NUMOD). This family also includes a Yarrowia lipolytica mobile group-II intron COX1-i1, also called intron alpha, encoding protein with reverse transcriptase activity. The group-II intron COX1-i1 may be involv ed both in the generation of the circular multimeric DNA molecules (senDNA alpha) which amplify during the senescence syndrome and in the generation of the site-specific deletion which accumulates in the premature-death syndrome.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102618198  13 GIYCIRNTVNNKCYIGKSVNIYERMRCHinlLNKRSKNENLYFINAWHKYGRNCFEYTVLEDC-VKDNDLLKERELYYIK 91
Cdd:cd10445     2 GIYIWINKINGKIYVGSSINLYKRLRSY---LNPSYLKKNSPILRALLKYGLSNFTLTILEYYnGENKEELLELEQYYID 78

                  ...
gi 1102618198  92 FYN 94
Cdd:cd10445    79 LLK 81

GIY-YIG domain of LuxR and ArsR family transcriptional regulators, and uncharacterized hypothetical proteins found in bacteria; The family includes some bacterial LuxR and ArsR family transcriptional regulators. The a C-terminal conserved domain shows sequence similarity to the N-terminal catalytic GIY-YIG domains of intron-encoded homing endonucleases. Besides, they have an N-terminally fused transcriptional regulators module, comprising the winged helix-turn-helix (wHTH) domain and uncharacterized domain DUF2087. At this point, they are distinct from GIY-YIG homing endonucleases, which typically contain a variety of C-terminally fused nuclease-associated modular DNA-binding domains (NUMODs). Moreover, some key residues relevant to catalysis in GIY-YIG endonucleases are mutanted or absent in this family, which suggests that members in this family might lose the catalytic function that GIY-YIG endonucleases possess. This family also includes many uncharacterized hypothetical proteins that consist of a standalone GIY-YIG like domain.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1102618198  13 GIYCIRNTVNNKCYIGKSVNIY---ERMRCHINLLNKRskneNLYFINAWHKYGRNCFEYTVLE 73
Cdd:cd10451    15 GVYAIRNTATGKVFIGSSPNLKgtlNRLRFQLNTGSHP----NKELQADWNEHGAEAFTFEVLE 74

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 1102618198  12 CGIYCIRNTVNNKCYIGKSVNIYERMRCHINLLNKRSKnenlyfinawHKYGRNCFEYTVLEDCvKDNDLLKERELYYIK 91
Cdd:pfam01541   2 GGIYIIRNKDNKLLYVGSTKNLERRLNQHNAGKGAKYT----------RGKGVEPFKLIYLEEF-PTKSEALELEKYLIK 70

                          90
                  ....*....|..
gi 1102618198  92 FYntidKKFGYN 103
Cdd:pfam01541  71 LY----RPNKYN 78