NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446299207|ref|WP_000377062|]
View 

MULTISPECIES: GIY-YIG nuclease family protein [Staphylococcus]

Protein Classification

GIY-YIG nuclease family protein( domain architecture ID 10179984)

GIY-YIG nuclease family protein is involved in many cellular processes, including DNA repair and recombination, transfer of mobile genetic elements, and restriction of incoming foreign DNA; similar to Lactococcus lactis UPF0213 protein YsiG

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
GIY-YIG_UPF0213 cd10456
The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific ...
 4-71 1.96e-34

The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; This family contains a group of uncharacterized proteins found mainly in bacteria and several in dsDNA viruses. Although their function roles have not been recognized, these proteins show significant sequence similarities with the N-terminal GIY-YIG endonuclease domain of structure-specific endonuclease subunit SLX1, which binds another structure-specific endonuclease subunit SLX4 to form an active heterodimeric SLX1-SLX4 complex. This complex functions as a 5' flap endonuclease in yeast, and has also been identified as a Holliday junction resolvase in human.


:

Pssm-ID: 198403  Cd Length: 68  Bit Score: 111.73  E-value: 1.96e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446299207  4 HFVYIVKCSDGSLYTGYAKDVNARIEKHNRGQGAKYTKIRRPVQLVYQETYETKSEALKREYEIKTYS 71
Cdd:cd10456   1 WYVYILRCADGSLYTGITTDLERRLAEHNSGKGAKYTRGRRPVKLVYSEEFDDRSEALKREYRIKKLS 68
 
Name Accession Description Interval E-value
GIY-YIG_UPF0213 cd10456
The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific ...
 4-71 1.96e-34

The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; This family contains a group of uncharacterized proteins found mainly in bacteria and several in dsDNA viruses. Although their function roles have not been recognized, these proteins show significant sequence similarities with the N-terminal GIY-YIG endonuclease domain of structure-specific endonuclease subunit SLX1, which binds another structure-specific endonuclease subunit SLX4 to form an active heterodimeric SLX1-SLX4 complex. This complex functions as a 5' flap endonuclease in yeast, and has also been identified as a Holliday junction resolvase in human.


Pssm-ID: 198403  Cd Length: 68  Bit Score: 111.73  E-value: 1.96e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446299207  4 HFVYIVKCSDGSLYTGYAKDVNARIEKHNRGQGAKYTKIRRPVQLVYQETYETKSEALKREYEIKTYS 71
Cdd:cd10456   1 WYVYILRCADGSLYTGITTDLERRLAEHNSGKGAKYTRGRRPVKLVYSEEFDDRSEALKREYRIKKLS 68
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
4-82 1.82e-33

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


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 109.83  E-value: 1.82e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446299207  4 HFVYIVKCSD-GSLYTGYAKDVNARIEKHNRGQGAKYTKIRRPVQLVYQETYETKSEALKREYEIKTYSRQKKLRLIKER 82
Cdd:COG2827   3 YYVYILRCADnGTLYTGVTNDLERRLAEHNSGKGAKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIEGD 82
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 1-82 5.71e-31

GIY-YIG nuclease superfamily protein; Validated


Pssm-ID: 178979  Cd Length: 86  Bit Score: 103.85  E-value: 5.71e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446299207  1 MDSHFVYIVKCSDGSLYTGYAKDVNARIEKHNRGQGAKYTKIRRPVQLVYQETYETKSEALKREYEIKTYSRQKKLRLIK 80
Cdd:PRK00329  4 MKPWFLYLLRCADGSLYTGITTDVERRFAQHQSGKGAKYTRGRPPLTLVFVEPVGDRSEALRAEYRFKQLTKKQKERLVA 83


                ..
gi 446299207 81 ER 82
Cdd:PRK00329 84 EG 85
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 4-77 8.65e-11

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: 52.34  E-value: 8.65e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446299207   4 HFVYIVKCSDGS-LYTGYAKDVNARIEKHNRGQGAKYT--KIRRPVQLVYQETYETKSEALKREYEIKTYSRQKKLR 77
Cdd:pfam01541  2 GGIYIIRNKDNKlLYVGSTKNLERRLNQHNAGKGAKYTrgKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPNKYN 78
GIYc smart00465
GIY-YIG type nucleases (URI domain);
3-80 5.37e-04

GIY-YIG type nucleases (URI domain);


Pssm-ID: 214677 [Multi-domain]  Cd Length: 84  Bit Score: 35.09  E-value: 5.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446299207    3 SHFVYIVKCSDGSLYTGYAKDVNARIEKHNRGQGAKYTKIR----RPVQLVYQETYETKSEALKREYE-IKTYSRQKKLR 77
Cdd:smart00465  2 PGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLLIDallkYGGNFEFIILESFDESALELEKYlIKEYKPKYNLL 81


                  ...
gi 446299207   78 LIK 80
Cdd:smart00465 82 LKG 84
 
Name Accession Description Interval E-value
GIY-YIG_UPF0213 cd10456
The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific ...
 4-71 1.96e-34

The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; This family contains a group of uncharacterized proteins found mainly in bacteria and several in dsDNA viruses. Although their function roles have not been recognized, these proteins show significant sequence similarities with the N-terminal GIY-YIG endonuclease domain of structure-specific endonuclease subunit SLX1, which binds another structure-specific endonuclease subunit SLX4 to form an active heterodimeric SLX1-SLX4 complex. This complex functions as a 5' flap endonuclease in yeast, and has also been identified as a Holliday junction resolvase in human.


Pssm-ID: 198403  Cd Length: 68  Bit Score: 111.73  E-value: 1.96e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446299207  4 HFVYIVKCSDGSLYTGYAKDVNARIEKHNRGQGAKYTKIRRPVQLVYQETYETKSEALKREYEIKTYS 71
Cdd:cd10456   1 WYVYILRCADGSLYTGITTDLERRLAEHNSGKGAKYTRGRRPVKLVYSEEFDDRSEALKREYRIKKLS 68
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
4-82 1.82e-33

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


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 109.83  E-value: 1.82e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446299207  4 HFVYIVKCSD-GSLYTGYAKDVNARIEKHNRGQGAKYTKIRRPVQLVYQETYETKSEALKREYEIKTYSRQKKLRLIKER 82
Cdd:COG2827   3 YYVYILRCADnGTLYTGVTNDLERRLAEHNSGKGAKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIEGD 82
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 1-82 5.71e-31

GIY-YIG nuclease superfamily protein; Validated


Pssm-ID: 178979  Cd Length: 86  Bit Score: 103.85  E-value: 5.71e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446299207  1 MDSHFVYIVKCSDGSLYTGYAKDVNARIEKHNRGQGAKYTKIRRPVQLVYQETYETKSEALKREYEIKTYSRQKKLRLIK 80
Cdd:PRK00329  4 MKPWFLYLLRCADGSLYTGITTDVERRFAQHQSGKGAKYTRGRPPLTLVFVEPVGDRSEALRAEYRFKQLTKKQKERLVA 83


                ..
gi 446299207 81 ER 82
Cdd:PRK00329 84 EG 85
GIY-YIG_unchar_3 cd10448
GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes ...
 5-81 3.23e-16

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: 66.36  E-value: 3.23e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446299207  5 FVYIV-KCSDGSLYTGYAKDVNARIEKHNRGQGAKYTKIRRPVQLVYQETYETKSEALKREYEIKTYSRQKKLRLIKE 81
Cdd:cd10448   2 YVYILaNKRNGTLYIGVTSDLIRRIYEHKEGLGSGFTSKYNVTRLVYYEEFEDIEEAIAREKQLKKWRRAWKINLIEK 79
GIY-YIG_SLX1_like cd10449
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 5-71 3.39e-16

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: 65.69  E-value: 3.39e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446299207  5 FVYIVKC-SDGSLYTGYAKDVNARIEKHNRGQGAKYTKiRRPVQLVYQETYETKSEALKREYEIKTYS 71
Cdd:cd10449   1 YVYILYSeKLDRYYIGYTSDLERRLEQHNSGKSKFTSK-YRPWELVYSEAFESKSEALKREKYLKSGK 67
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 4-77 8.65e-11

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: 52.34  E-value: 8.65e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446299207   4 HFVYIVKCSDGS-LYTGYAKDVNARIEKHNRGQGAKYT--KIRRPVQLVYQETYETKSEALKREYEIKTYSRQKKLR 77
Cdd:pfam01541  2 GGIYIIRNKDNKlLYVGSTKNLERRLNQHNAGKGAKYTrgKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPNKYN 78
GIY-YIG_SF cd00719
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ...
 5-70 2.31e-07

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: 43.51  E-value: 2.31e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446299207  5 FVYIVKCSDGSL-YTGYAKDVNARIEKHNRGQGAKYTKIRRPVQLVYQETYET-KSEALKREYEIKTY 70
Cdd:cd00719   1 GVYVLYDEDNGLiYVGQTKNLRNRIKEHLRKQRSDWTKGLKPFEILYLEVAPEaESELLDLEAALIKK 68
GIY-YIG_SLX1 cd10455
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 4-65 7.10e-06

Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic 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: 198402  Cd Length: 76  Bit Score: 39.91  E-value: 7.10e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446299207  4 HFVYIVKCSD----GSLYTGYAKDVNARIEKHNRG--QGAKYTKIRRP---VQLVYqeTYETKSEALKREY 65
Cdd:cd10455   2 YGVYLLRSLNpkykGRTYIGFTVNPPRRLRQHNGElkGGAKKTSRKRPwemVLIVH--GFPSKVAALQFEW 70
GIYc smart00465
GIY-YIG type nucleases (URI domain);
3-80 5.37e-04

GIY-YIG type nucleases (URI domain);


Pssm-ID: 214677 [Multi-domain]  Cd Length: 84  Bit Score: 35.09  E-value: 5.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446299207    3 SHFVYIVKCSDGSLYTGYAKDVNARIEKHNRGQGAKYTKIR----RPVQLVYQETYETKSEALKREYE-IKTYSRQKKLR 77
Cdd:smart00465  2 PGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLLIDallkYGGNFEFIILESFDESALELEKYlIKEYKPKYNLL 81


                  ...
gi 446299207   78 LIK 80
Cdd:smart00465 82 LKG 84
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH