GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes a group of uncharacterized bacterial 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 and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482993602  5 YYVYIMTNKYNNVLYVGVTNDLQRRVYEHREKLVAGFTRKYNVDKLVWYETHENPESAILREKQIKDRPRAKKIALVEAY 84
Cdd:cd10448    1 YYVYILANKRNGTLYIGVTSDLIRRIYEHKEGLGSGFTSKYNVTRLVYYEEFEDIEEAIAREKQLKKWRRAWKINLIEKM 80

                 ....*..
gi 1482993602 85 NPEYIDL 91
Cdd:cd10448   81 NPDWKDL 87

GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes a group of uncharacterized bacterial 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 and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482993602  5 YYVYIMTNKYNNVLYVGVTNDLQRRVYEHREKLVAGFTRKYNVDKLVWYETHENPESAILREKQIKDRPRAKKIALVEAY 84
Cdd:cd10448    1 YYVYILANKRNGTLYIGVTSDLIRRIYEHKEGLGSGFTSKYNVTRLVYYEEFEDIEEAIAREKQLKKWRRAWKINLIEKM 80

                 ....*..
gi 1482993602 85 NPEYIDL 91
Cdd:cd10448   81 NPDWKDL 87

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 1482993602  4 QYYVYIMTNKYNNVLYVGVTNDLQRRVYEHREKLVAGFTRKYNVD--KLVWYETHENPESAILREKQIKDRPRAKKI 78
Cdd:pfam01541  1 KGGIYIIRNKDNKLLYVGSTKNLERRLNQHNAGKGAKYTRGKGVEpfKLIYLEEFPTKSEALELEKYLIKLYRPNKY 77

GIY-YIG type nucleases (URI domain);

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1482993602   6 YVYIMTNKYNNVLYVGVTNDLQRRVYEHREKLVAGFTRKYNVDK----LVWYETHENPESAILREKQIKDRPRAKK 77
Cdd:smart00465  3 GVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLLIDALLKyggnFEFIILESFDESALELEKYLIKEYKPKY 78

GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes a group of uncharacterized bacterial 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 and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482993602  5 YYVYIMTNKYNNVLYVGVTNDLQRRVYEHREKLVAGFTRKYNVDKLVWYETHENPESAILREKQIKDRPRAKKIALVEAY 84
Cdd:cd10448    1 YYVYILANKRNGTLYIGVTSDLIRRIYEHKEGLGSGFTSKYNVTRLVYYEEFEDIEEAIAREKQLKKWRRAWKINLIEKM 80

                 ....*..
gi 1482993602 85 NPEYIDL 91
Cdd:cd10448   81 NPDWKDL 87

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 1482993602  4 QYYVYIMTNKYNNVLYVGVTNDLQRRVYEHREKLVAGFTRKYNVD--KLVWYETHENPESAILREKQIKDRPRAKKI 78
Cdd:pfam01541  1 KGGIYIIRNKDNKLLYVGSTKNLERRLNQHNAGKGAKYTRGKGVEpfKLIYLEEFPTKSEALELEKYLIKLYRPNKY 77

GIY-YIG nuclease superfamily protein; Validated

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482993602  1 MSKQYYVYIMTNKyNNVLYVGVTNDLQRRVYEHREKLVAGFTRKYNVDKLVWYETHENPESAILREKQIKDRPRAKKIAL 80
Cdd:PRK00329   3 EMKPWFLYLLRCA-DGSLYTGITTDVERRFAQHQSGKGAKYTRGRPPLTLVFVEPVGDRSEALRAEYRFKQLTKKQKERL 81

                 ....
gi 1482993602 81 VEAY 84
Cdd:PRK00329  82 VAEG 85

Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its homologs; Structure-specific endonuclease subunit SLX1 is a highly conserved protein from yeast to human, with an N-terminal GIY-YIG endonuclease domain and a C-terminal PHD-type zinc finger postulated to mediate protein-protein or protein-DNA interaction. SLX1 forms active heterodimeric complexes with its SLX4 partner, which has additional roles in the DNA damage response that are distinct from the function of the heterodimeric SLX1-SLX4 nuclease. In yeast, the SLX1-SLX4 complex functions as a 5' flap endonuclease that maintains ribosomal DNA copy number, where SLX1 and SLX4 are shown to be catalytic and regulatory subunits, respectively. This endonuclease introduces single-strand cuts in duplex DNA on the 3' side of junctions with single-strand DNA. In addition to 5' flap endonuclease activity, human SLX1-SLX4 complex has been identified as a Holliday junction resolvase that promotes symmetrical cleavage of static and migrating Holliday junctions. SLX1 also associates with MUS81, EME1, C20orf94, PLK1, and ERCC1. Some eukaryotic SLX1 homologs lack the zinc finger domain, but possess intrinsically unstructured extensions of unknown function. These unstructured segments might be involved in interactions with other proteins.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1482993602  6 YVYIMTNKYNNVLYVGVTNDLQRRVYEHREKLVAGFTRKYNVdKLVWYETHENPESAILREKQIK 70
Cdd:cd10449    1 YVYILYSEKLDRYYIGYTSDLERRLEQHNSGKSKFTSKYRPW-ELVYSEAFESKSEALKREKYLK 64

Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; UvrC is essential for nucleotide excision repair (NER). The N-terminal catalytic GIY-YIG domain of UvrC (also known as Uri domain) is responsible for the 3' incision reaction and the C-terminal half of UvrC, consisting of an UvrB-binding domain (UvrBb), EndoV-like nuclease domain and a helix-hairpin-helix (HhH) DNA-binding domain, contains the residues involved in 5' incision. The N- and C-terminal regions are joined by a common Cys-rich domain containing four conserved Cys residues. Besides UvrC, protein Cho (UvrC homolog) serves as a second endonuclease in E. coli NER. Cho contains GIY-YIG motif followed by a Cys-rich region and shares sequence homology with the N-terminal half of UvrC. It is capable of incising the DNA at the 3' side of a lesion in the presence of the UvrA and UvrB proteins during NER. The C-terminal half of Cho is a unique uncharacterized domain, which is distinct from that of UvrC. Moreover, unlike UvrC, Cho does not require the UvrC-binding domain of UvrB for the 3' incision reaction, which might cause the shift in incision position and the difference in incision efficiencies between Cho and UvrC on different damaged substrates. Due to this, the range of NER in E. coli can be broadened by combining action of Cho and UvrC. This family also includes many uncharacterized epsilon proofreading subunits of DNA polymerase III, which have an additional N-terminal ExoIII domain and a 3'-5' exonuclease domain homolog, fused to an UvrC-like region or a Cho-like region. The UvrC-like region includes a GIY-YIG motif, followed by a Cys-rich region, and an UvrB-binding domain (UvrBb), but lacks the EndoV-like nuclease domain and the helix-hairpin-helix (HhH) DNA-binding domain. The Cho-like region consists of a GIY-YIG motif, followed by the Cys-rich region, and the unique uncharacterized domain presenting in the C-terminal half of Cho. Some family members may not carry the Cys-rich region. This family also includes a specific Cho-like protein from G. violaceus, which possesses only UvrBb domain at the C-terminus, but lacks the additional N-terminal ExoIII domain. The oother two remote homologs of UvrC, Bacillus-I and -II, are included in this family as well. Both of them contain a GIY-YIG domain, but no Cys-rich region. Moreover, the whole C-terminal region of Bacillus-I is replaces by an unknown domain, and Bacillus-II possesses another unknown N-terminal extension.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1482993602  7 VYIMTNKYNNVLYVGVTNDLQRRVYEH-REKLVAGFTRKY--NVDKLVWYEThENPESAILREKQ-IKD-RPR 74
Cdd:cd10434    7 VYLFKDADGEVLYVGKAKNLRKRVSSYfTGERHSPKTRRLveEIRDIEYIVT-DSELEALLLEANlIKKyKPR 78