N-terminal catalytic GIY-YIG domain of bacteriophage T4 segABCDEFG gene encoding proteins; The prototypes of Seg family are proteins SegA, B, C, D, E, F, and G encoded by five seg genes segA, B, C, D, E, F, and G in the bacteriophage T4 genome, respectively. SegA, B, C, D, E, F, and G are not encoded by introns, but free-standing homologs of the GIY-YIG family of endonucleases encoded by group I introns, which are thought to initiate the homing of their own intron by cleaving the intronless DNA at or near the site of insertion. Both phage T4 intron-encoded and free-standing GIY-YIG endonucleases contribute to the exclusion of T2 markers from the progeny of mixed infections. SegA, encoded by the bacteriophage T4 segA gene, is a double-strand DNA endonulcease with a hierarchy of site specificity. The cleavage site of SegA is located in the uvsX gene of T4. Its cleaving activity requires the presence of Mg2+ and can be stimulated by the presence of ATP or ATPgammaS. Bacteriophage T4 segB gene encoding protein SegB is a site-specific endonuclease that recognizes a 27-bp sequence, cleaves DNA by introdu cing double-strand breaks in the adjacent gene 56 of T2 during mixed infection in the presence of Mg2+, Mn2+, or Ca2+ cations, and produces mostly 3' 2-nt protruding ends at its DNA cleavage site. It functions as a homing endonuclease to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages. Bacteriophage T4 segE gene encoding SegE is a site-specific endonuclease that preferentially cleaves DNA in a site located at the 5' end of the uvsW gene in the RB30 genome. It is responsible for a non-reciprocal genetic exchange between T-even-related phages. Bacteriophage T4 gene 69 encoding SegF is a site-specific double-strand DNA endonuclease that promotes marker exclusion. It preferentially introduces a double-strand break in the adjacent T2 gene 56 over T4 gene 56 both in vitro and in vivo during mixed infection, which results in the replacement of T2 gene 56 by T4 gene 56 in a process similar to group I intron homing. The cleavage site is located 210- and 212-bp upstream from its insertion site. Bacteriophage T4 segG gene (formerly gene 32.1) encoding SegG (also known as F-TevIV) is a double-strand DNA endonuclease adjacent to gene 32 of phage T4 that promotes marker exclusion. Although it is absent from phage T2, SegG preferentially introduces a double-strand break in T2 gene 32 during mixed infection, which results in replacement of T2 genetic markers by the corresponding T4 markers. The cleavage site is located 332- and 334-bp from its insertion site.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930297021   4 YIYKITNKINNKIYIGAHS---TKNLDDGYMGSGKLLKRAQDKYGIENFSKEILEYFDDKESMLEAEKNIVTEEFLNRPD 80
Cdd:cd10444     1 FVYRITNLTTGKIYIGKHHsciTNSLWDDYWGSGKILKNLIKKYGGENFSREILKVFPSREEAYEAEALLISELNVKSPN 80

                  ....*
gi 1930297021  81 VYNLK 85
Cdd:cd10444    81 CYNIA 85

N-terminal catalytic GIY-YIG domain of bacteriophage T4 segABCDEFG gene encoding proteins; The prototypes of Seg family are proteins SegA, B, C, D, E, F, and G encoded by five seg genes segA, B, C, D, E, F, and G in the bacteriophage T4 genome, respectively. SegA, B, C, D, E, F, and G are not encoded by introns, but free-standing homologs of the GIY-YIG family of endonucleases encoded by group I introns, which are thought to initiate the homing of their own intron by cleaving the intronless DNA at or near the site of insertion. Both phage T4 intron-encoded and free-standing GIY-YIG endonucleases contribute to the exclusion of T2 markers from the progeny of mixed infections. SegA, encoded by the bacteriophage T4 segA gene, is a double-strand DNA endonulcease with a hierarchy of site specificity. The cleavage site of SegA is located in the uvsX gene of T4. Its cleaving activity requires the presence of Mg2+ and can be stimulated by the presence of ATP or ATPgammaS. Bacteriophage T4 segB gene encoding protein SegB is a site-specific endonuclease that recognizes a 27-bp sequence, cleaves DNA by introdu cing double-strand breaks in the adjacent gene 56 of T2 during mixed infection in the presence of Mg2+, Mn2+, or Ca2+ cations, and produces mostly 3' 2-nt protruding ends at its DNA cleavage site. It functions as a homing endonuclease to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages. Bacteriophage T4 segE gene encoding SegE is a site-specific endonuclease that preferentially cleaves DNA in a site located at the 5' end of the uvsW gene in the RB30 genome. It is responsible for a non-reciprocal genetic exchange between T-even-related phages. Bacteriophage T4 gene 69 encoding SegF is a site-specific double-strand DNA endonuclease that promotes marker exclusion. It preferentially introduces a double-strand break in the adjacent T2 gene 56 over T4 gene 56 both in vitro and in vivo during mixed infection, which results in the replacement of T2 gene 56 by T4 gene 56 in a process similar to group I intron homing. The cleavage site is located 210- and 212-bp upstream from its insertion site. Bacteriophage T4 segG gene (formerly gene 32.1) encoding SegG (also known as F-TevIV) is a double-strand DNA endonuclease adjacent to gene 32 of phage T4 that promotes marker exclusion. Although it is absent from phage T2, SegG preferentially introduces a double-strand break in T2 gene 32 during mixed infection, which results in replacement of T2 genetic markers by the corresponding T4 markers. The cleavage site is located 332- and 334-bp from its insertion site.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930297021   4 YIYKITNKINNKIYIGAHS---TKNLDDGYMGSGKLLKRAQDKYGIENFSKEILEYFDDKESMLEAEKNIVTEEFLNRPD 80
Cdd:cd10444     1 FVYRITNLTTGKIYIGKHHsciTNSLWDDYWGSGKILKNLIKKYGGENFSREILKVFPSREEAYEAEALLISELNVKSPN 80

                  ....*
gi 1930297021  81 VYNLK 85
Cdd:cd10444    81 CYNIA 85

GIY-YIG type nucleases (URI domain);

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930297021    4 YIYKITNKINNKIYIGA--HSTKNLDDGYMGS--GKLLKRAQDKYGiENFSKEILEYFDdkESMLEAEKNIVTEEFlnrp 79
Cdd:smart00465   3 GVYYITNKKNGKLYVGKakNLRNRLKRHFSGSrkGRLLIDALLKYG-GNFEFIILESFD--ESALELEKYLIKEYK---- 75

                   ....*....
gi 1930297021   80 DVYNLKLGG 88
Cdd:smart00465  76 PKYNLLLKG 84

N-terminal catalytic GIY-YIG domain of bacteriophage T4 segABCDEFG gene encoding proteins; The prototypes of Seg family are proteins SegA, B, C, D, E, F, and G encoded by five seg genes segA, B, C, D, E, F, and G in the bacteriophage T4 genome, respectively. SegA, B, C, D, E, F, and G are not encoded by introns, but free-standing homologs of the GIY-YIG family of endonucleases encoded by group I introns, which are thought to initiate the homing of their own intron by cleaving the intronless DNA at or near the site of insertion. Both phage T4 intron-encoded and free-standing GIY-YIG endonucleases contribute to the exclusion of T2 markers from the progeny of mixed infections. SegA, encoded by the bacteriophage T4 segA gene, is a double-strand DNA endonulcease with a hierarchy of site specificity. The cleavage site of SegA is located in the uvsX gene of T4. Its cleaving activity requires the presence of Mg2+ and can be stimulated by the presence of ATP or ATPgammaS. Bacteriophage T4 segB gene encoding protein SegB is a site-specific endonuclease that recognizes a 27-bp sequence, cleaves DNA by introdu cing double-strand breaks in the adjacent gene 56 of T2 during mixed infection in the presence of Mg2+, Mn2+, or Ca2+ cations, and produces mostly 3' 2-nt protruding ends at its DNA cleavage site. It functions as a homing endonuclease to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages. Bacteriophage T4 segE gene encoding SegE is a site-specific endonuclease that preferentially cleaves DNA in a site located at the 5' end of the uvsW gene in the RB30 genome. It is responsible for a non-reciprocal genetic exchange between T-even-related phages. Bacteriophage T4 gene 69 encoding SegF is a site-specific double-strand DNA endonuclease that promotes marker exclusion. It preferentially introduces a double-strand break in the adjacent T2 gene 56 over T4 gene 56 both in vitro and in vivo during mixed infection, which results in the replacement of T2 gene 56 by T4 gene 56 in a process similar to group I intron homing. The cleavage site is located 210- and 212-bp upstream from its insertion site. Bacteriophage T4 segG gene (formerly gene 32.1) encoding SegG (also known as F-TevIV) is a double-strand DNA endonuclease adjacent to gene 32 of phage T4 that promotes marker exclusion. Although it is absent from phage T2, SegG preferentially introduces a double-strand break in T2 gene 32 during mixed infection, which results in replacement of T2 genetic markers by the corresponding T4 markers. The cleavage site is located 332- and 334-bp from its insertion site.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930297021   4 YIYKITNKINNKIYIGAHS---TKNLDDGYMGSGKLLKRAQDKYGIENFSKEILEYFDDKESMLEAEKNIVTEEFLNRPD 80
Cdd:cd10444     1 FVYRITNLTTGKIYIGKHHsciTNSLWDDYWGSGKILKNLIKKYGGENFSREILKVFPSREEAYEAEALLISELNVKSPN 80

                  ....*
gi 1930297021  81 VYNLK 85
Cdd:cd10444    81 CYNIA 85

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 1930297021   3 YYIYKITNKINNKIYIGahSTKNLDD----------GYMGSGKLLKRAQDKYGIENFSKEILEYFDDKESMLEAEK 68
Cdd:cd10437     1 SGIYKITNLENGKIYIG--SSKNILKrlsqhkrdlkAGKHHNKKLQRDFNKYGEENFEFTILEEGEEIEKLLELEQ 74

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 1930297021   5 IYKITNKINNKIYIGahSTKNLDD--------GYMGSGKLLKRAQDKYGIENFSKEILEYFD--DKESMLEAE 67
Cdd:cd10445     3 IYIWINKINGKIYVG--SSINLYKrlrsylnpSYLKKNSPILRALLKYGLSNFTLTILEYYNgeNKEELLELE 73

Putative endonuclease segE, GIY-YIG domain; This domain family is found in viruses. Proteins containing this domain are typically between 147 and 298 amino acids in length. They have a GIY-YIG domain at the N-terminal, which suggests they are likely to be endonucleases. Included in this family is the Putative endonuclease segE from Bacteriophage T4.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930297021   2 FYYIYKITNKINNKIYIGA---HSTKNLDDG------------YMGSGKLLKRAQDKYGIENFSKEILEYFDDKESMLEA 66
Cdd:pfam19835  17 FGFVYLITNLENGKKYIGRkyfWKKRKPPGKkrkvksesdwkkYYGSSDELKEDIKKYGKENFKREILSLHKTKGKVNYE 96

                  .
gi 1930297021  67 E 67
Cdd:pfam19835  97 E 97

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1930297021   2 FYYIYKITNKINNKIYIGahSTKNLD----DGYMGSGKLLKRaqdKYGIENFSKEILEYFDDKESMLEAEKNI 70
Cdd:pfam01541   1 KGGIYIIRNKDNKLLYVG--STKNLErrlnQHNAGKGAKYTR---GKGVEPFKLIYLEEFPTKSEALELEKYL 68