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Conserved domains on  [gi|818609378|gb|KKS58250|]
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MAG: endonuclease [Parcubacteria group bacterium GW2011_GWA2_42_35]

Protein Classification

GIY-YIG nuclease family protein( domain architecture ID 10179946)

GIY-YIG nuclease family protein

CATH:  3.40.1440.10
Gene Ontology:  GO:0004518
PubMed:  16646971
SCOP:  3000597

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
GIY-YIG_SLX1_like cd10449
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 3-70 9.72e-20

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.


:

Pssm-ID: 198396  Cd Length: 67  Bit Score: 74.94  E-value: 9.72e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818609378  3 YVYVLKSLKNGKRYVGSTDLLpEERLKKHNYGSNQFTKRNGPFELVHQESYSNKTEARKRENFLKSGA 70
Cdd:cd10449   1 YVYILYSEKLDRYYIGYTSDL-ERRLEQHNSGKSKFTSKYRPWELVYSEAFESKSEALKREKYLKSGK 67
 
Name Accession Description Interval E-value
GIY-YIG_SLX1_like cd10449
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 3-70 9.72e-20

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.


Pssm-ID: 198396  Cd Length: 67  Bit Score: 74.94  E-value: 9.72e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818609378  3 YVYVLKSLKNGKRYVGSTDLLpEERLKKHNYGSNQFTKRNGPFELVHQESYSNKTEARKRENFLKSGA 70
Cdd:cd10449   1 YVYILYSEKLDRYYIGYTSDL-ERRLEQHNSGKSKFTSKYRPWELVYSEAFESKSEALKREKYLKSGK 67
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
1-81 1.35e-19

Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 74.78  E-value: 1.35e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818609378  1 MSYVYVLKSLKNGKRYVGSTDLLpEERLKKHNYG-SNQFTKRNGPFELVHQESYSNKTEARKRENFLKSGAGRKYLDKIL 79
Cdd:COG2827   2 MYYVYILRCADNGTLYTGVTNDL-ERRLAEHNSGkGAKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIE 80


                ..
gi 818609378 80 EQ 81
Cdd:COG2827  81 GD 82
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 1-67 4.29e-09

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.


Pssm-ID: 426314 [Multi-domain]  Cd Length: 78  Bit Score: 48.11  E-value: 4.29e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818609378   1 MSYVYVLKSLKNGKRYVGSTDLLpEERLKKHNYGSNQFTKRN---GPFELVHQESYSNKTEARKRENFLK 67
Cdd:pfam01541  1 KGGIYIIRNKDNKLLYVGSTKNL-ERRLNQHNAGKGAKYTRGkgvEPFKLIYLEEFPTKSEALELEKYLI 69
 
Name Accession Description Interval E-value
GIY-YIG_SLX1_like cd10449
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 3-70 9.72e-20

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.


Pssm-ID: 198396  Cd Length: 67  Bit Score: 74.94  E-value: 9.72e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818609378  3 YVYVLKSLKNGKRYVGSTDLLpEERLKKHNYGSNQFTKRNGPFELVHQESYSNKTEARKRENFLKSGA 70
Cdd:cd10449   1 YVYILYSEKLDRYYIGYTSDL-ERRLEQHNSGKSKFTSKYRPWELVYSEAFESKSEALKREKYLKSGK 67
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
1-81 1.35e-19

Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 74.78  E-value: 1.35e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818609378  1 MSYVYVLKSLKNGKRYVGSTDLLpEERLKKHNYG-SNQFTKRNGPFELVHQESYSNKTEARKRENFLKSGAGRKYLDKIL 79
Cdd:COG2827   2 MYYVYILRCADNGTLYTGVTNDL-ERRLAEHNSGkGAKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIE 80


                ..
gi 818609378 80 EQ 81
Cdd:COG2827  81 GD 82
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 1-67 4.29e-09

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.


Pssm-ID: 426314 [Multi-domain]  Cd Length: 78  Bit Score: 48.11  E-value: 4.29e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818609378   1 MSYVYVLKSLKNGKRYVGSTDLLpEERLKKHNYGSNQFTKRN---GPFELVHQESYSNKTEARKRENFLK 67
Cdd:pfam01541  1 KGGIYIIRNKDNKLLYVGSTKNL-ERRLNQHNAGKGAKYTRGkgvEPFKLIYLEEFPTKSEALELEKYLI 69
GIY-YIG_unchar_3 cd10448
GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes ...
 2-67 1.29e-05

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.


Pssm-ID: 198395  Cd Length: 87  Bit Score: 39.40  E-value: 1.29e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 818609378  2 SYVYVLKSLKNGKRYVGSTDLLpEERLKKHNYGSNQ-FTKRNGPFELVHQESYSNKTEARKRENFLK 67
Cdd:cd10448   1 YYVYILANKRNGTLYIGVTSDL-IRRIYEHKEGLGSgFTSKYNVTRLVYYEEFEDIEEAIAREKQLK 66
GIY-YIG_SF cd00719
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ...
 3-67 3.86e-04

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.


Pssm-ID: 198380 [Multi-domain]  Cd Length: 69  Bit Score: 35.03  E-value: 3.86e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 818609378  3 YVYVLKSLKNGKRYVGSTDLLpEERLKKHNYGSNQ-FTKRNGPFEL-VHQESYSNKTEARKRENFLK 67
Cdd:cd00719   1 GVYVLYDEDNGLIYVGQTKNL-RNRIKEHLRKQRSdWTKGLKPFEIlYLEVAPEAESELLDLEAALI 66
GIY-YIG_HE_Tlr8p_PBC-V_like cd10443
GIY-YIG domain of uncharacterized hypothetical protein found in phycodnavirus PBCV-1 DNA virus, ...
 3-31 1.66e-03

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.


Pssm-ID: 198390  Cd Length: 90  Bit Score: 33.81  E-value: 1.66e-03
                        10        20
                ....*....|....*....|....*....
gi 818609378  3 YVYVLKSLKNGKRYVGSTDLLPEERLKKH 31
Cdd:cd10443   2 VIYKITNPINGKVYIGQTTRTLEERLKQH 30
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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