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Conserved domains on  [gi|489335759|ref|WP_003242983|]
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MULTISPECIES: GIY-YIG nuclease family protein [Bacillus]

Protein Classification

GIY-YIG nuclease family protein( domain architecture ID 10791911)

GIY-YIG nuclease family protein similar to DNA damage response nuclease YhbQ

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
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 1-85 6.21e-42

GIY-YIG nuclease superfamily protein; Validated


:

Pssm-ID: 178979  Cd Length: 86  Bit Score: 132.35  E-value: 6.21e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489335759  1 METNNHFFYVVKCKDNSWYAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFSTKREAMQAEYYFKKLTRKKKELY 80
Cdd:PRK00329  2 AEMKPWFLYLLRCADGSLYTGITTDVERRFAQHQSGKGAKYTRGRPPLTLVFVEPVGDRSEALRAEYRFKQLTKKQKERL 81


                ....*
gi 489335759 81 IEEKR 85
Cdd:PRK00329 82 VAEGE 86
 
Name Accession Description Interval E-value
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 1-85 6.21e-42

GIY-YIG nuclease superfamily protein; Validated


Pssm-ID: 178979  Cd Length: 86  Bit Score: 132.35  E-value: 6.21e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489335759  1 METNNHFFYVVKCKDNSWYAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFSTKREAMQAEYYFKKLTRKKKELY 80
Cdd:PRK00329  2 AEMKPWFLYLLRCADGSLYTGITTDVERRFAQHQSGKGAKYTRGRPPLTLVFVEPVGDRSEALRAEYRFKQLTKKQKERL 81


                ....*
gi 489335759 81 IEEKR 85
Cdd:PRK00329 82 VAEGE 86
GIY-YIG_UPF0213 cd10456
The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific ...
 6-73 1.08e-33

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: 110.58  E-value: 1.08e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489335759  6 HFFYVVKCKDNSWYAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFSTKREAMQAEYYFKKLT 73
Cdd:cd10456   1 WYVYILRCADGSLYTGITTDLERRLAEHNSGKGAKYTRGRRPVKLVYSEEFDDRSEALKREYRIKKLS 68
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
5-83 2.12e-31

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


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 105.21  E-value: 2.12e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489335759  5 NHFFYVVKCKDN-SWYAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFSTKREAMQAEYYFKKLTRKKKELYIEE 83
Cdd:COG2827   2 MYYVYILRCADNgTLYTGVTNDLERRLAEHNSGKGAKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIEG 81
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 5-78 3.78e-14

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: 61.59  E-value: 3.78e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489335759   5 NHFFYVVKCKDNS-WYAGYTNDLHKRVKTHNDGKGAKYTKVR--RPVELIFAESFSTKREAMQAEYYFKKLTRKKKE 78
Cdd:pfam01541  1 KGGIYIIRNKDNKlLYVGSTKNLERRLNQHNAGKGAKYTRGKgvEPFKLIYLEEFPTKSEALELEKYLIKLYRPNKY 77
GIYc smart00465
GIY-YIG type nucleases (URI domain);
7-82 1.21e-04

GIY-YIG type nucleases (URI domain);


Pssm-ID: 214677 [Multi-domain]  Cd Length: 84  Bit Score: 37.40  E-value: 1.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489335759    7 FFYVVKCKDNSWYAGYTNDLHKRVKTHNDGKgakyTKVRRPVELIFAESFSTKRE--------AMQAEYYFKKLTRKKKE 78
Cdd:smart00465  4 VYYITNKKNGKLYVGKAKNLRNRLKRHFSGS----RKGRLLIDALLKYGGNFEFIilesfdesALELEKYLIKEYKPKYN 79


                  ....
gi 489335759   79 LYIE 82
Cdd:smart00465 80 LLLK 83
 
Name Accession Description Interval E-value
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 1-85 6.21e-42

GIY-YIG nuclease superfamily protein; Validated


Pssm-ID: 178979  Cd Length: 86  Bit Score: 132.35  E-value: 6.21e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489335759  1 METNNHFFYVVKCKDNSWYAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFSTKREAMQAEYYFKKLTRKKKELY 80
Cdd:PRK00329  2 AEMKPWFLYLLRCADGSLYTGITTDVERRFAQHQSGKGAKYTRGRPPLTLVFVEPVGDRSEALRAEYRFKQLTKKQKERL 81


                ....*
gi 489335759 81 IEEKR 85
Cdd:PRK00329 82 VAEGE 86
GIY-YIG_UPF0213 cd10456
The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific ...
 6-73 1.08e-33

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: 110.58  E-value: 1.08e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489335759  6 HFFYVVKCKDNSWYAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFSTKREAMQAEYYFKKLT 73
Cdd:cd10456   1 WYVYILRCADGSLYTGITTDLERRLAEHNSGKGAKYTRGRRPVKLVYSEEFDDRSEALKREYRIKKLS 68
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
5-83 2.12e-31

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


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 105.21  E-value: 2.12e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489335759  5 NHFFYVVKCKDN-SWYAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFSTKREAMQAEYYFKKLTRKKKELYIEE 83
Cdd:COG2827   2 MYYVYILRCADNgTLYTGVTNDLERRLAEHNSGKGAKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIEG 81
GIY-YIG_SLX1_like cd10449
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 7-71 1.55e-14

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: 62.22  E-value: 1.55e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489335759  7 FFYVVKC-KDNSWYAGYTNDLHKRVKTHNDGKGAKYTKvRRPVELIFAESFSTKREAMQAEYYFKK 71
Cdd:cd10449   1 YVYILYSeKLDRYYIGYTSDLERRLEQHNSGKSKFTSK-YRPWELVYSEAFESKSEALKREKYLKS 65
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 5-78 3.78e-14

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: 61.59  E-value: 3.78e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489335759   5 NHFFYVVKCKDNS-WYAGYTNDLHKRVKTHNDGKGAKYTKVR--RPVELIFAESFSTKREAMQAEYYFKKLTRKKKE 78
Cdd:pfam01541  1 KGGIYIIRNKDNKlLYVGSTKNLERRLNQHNAGKGAKYTRGKgvEPFKLIYLEEFPTKSEALELEKYLIKLYRPNKY 77
GIY-YIG_unchar_3 cd10448
GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes ...
 19-84 1.37e-07

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: 45.18  E-value: 1.37e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489335759 19 YAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFSTKREAMQAEYYFKKLTRKKKELYIEEK 84
Cdd:cd10448  15 YIGVTSDLIRRIYEHKEGLGSGFTSKYNVTRLVYYEEFEDIEEAIAREKQLKKWRRAWKINLIEKM 80
GIY-YIG_SF cd00719
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ...
 9-73 9.22e-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: 42.35  E-value: 9.22e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489335759  9 YVVKCKDN-SWYAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFST-KREAMQAEYYFKKLT 73
Cdd:cd00719   3 YVLYDEDNgLIYVGQTKNLRNRIKEHLRKQRSDWTKGLKPFEILYLEVAPEaESELLDLEAALIKKL 69
GIY-YIG_SLX1 cd10455
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 19-67 3.20e-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: 41.06  E-value: 3.20e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 489335759 19 YAGYTNDLHKRVKTHNDG--KGAKYTKVRRPVELI-FAESFSTKREAMQAEY 67
Cdd:cd10455  19 YIGFTVNPPRRLRQHNGElkGGAKKTSRKRPWEMVlIVHGFPSKVAALQFEW 70
GIYc smart00465
GIY-YIG type nucleases (URI domain);
7-82 1.21e-04

GIY-YIG type nucleases (URI domain);


Pssm-ID: 214677 [Multi-domain]  Cd Length: 84  Bit Score: 37.40  E-value: 1.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489335759    7 FFYVVKCKDNSWYAGYTNDLHKRVKTHNDGKgakyTKVRRPVELIFAESFSTKRE--------AMQAEYYFKKLTRKKKE 78
Cdd:smart00465  4 VYYITNKKNGKLYVGKAKNLRNRLKRHFSGS----RKGRLLIDALLKYGGNFEFIilesfdesALELEKYLIKEYKPKYN 79


                  ....
gi 489335759   79 LYIE 82
Cdd:smart00465 80 LLLK 83
 
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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