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Conserved domains on  [gi|1083736607|gb|OGI19241|]
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MAG: hypothetical protein A3J06_04325 [Candidatus Moranbacteria bacterium RIFCSPLOWO2_02_FULL_48_19]

Protein Classification

GIY-YIG nuclease family protein( domain architecture ID 10006682)

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 Clostridium perfringens UPF0213 protein CPE1444

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
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
1-81 8.27e-21

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


:

Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 77.86  E-value: 8.27e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083736607  1 MKGYIYILLSLKDYKTYTGSTDNLEKRLKEHHNGKC-KATVNRRPLQLIYSEKIDSLDEARKREKYFKTASGRRALKKIF 79
Cdd:COG2827    1 MMYYVYILRCADNGTLYTGVTNDLERRLAEHNSGKGaKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIE 80


                 ..
gi 1083736607 80 ED 81
Cdd:COG2827   81 GD 82
 
Name Accession Description Interval E-value
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
1-81 8.27e-21

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


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 77.86  E-value: 8.27e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083736607  1 MKGYIYILLSLKDYKTYTGSTDNLEKRLKEHHNGKC-KATVNRRPLQLIYSEKIDSLDEARKREKYFKTASGRRALKKIF 79
Cdd:COG2827    1 MMYYVYILRCADNGTLYTGVTNDLERRLAEHNSGKGaKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIE 80


                 ..
gi 1083736607 80 ED 81
Cdd:COG2827   81 GD 82
GIY-YIG_SLX1_like cd10449
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 4-70 8.78e-19

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: 72.24  E-value: 8.78e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1083736607  4 YIYILLSLKDYKTYTGSTDNLEKRLKEHHNGKCKATVNRRPLQLIYSEKIDSLDEARKREKYFKTAS 70
Cdd:cd10449    1 YVYILYSEKLDRYYIGYTSDLERRLEQHNSGKSKFTSKYRPWELVYSEAFESKSEALKREKYLKSGK 67
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 2-73 1.34e-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: 54.65  E-value: 1.34e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083736607  2 KGYIYILLSLKDYKTYTGSTDNLEKRLKEH---HNGKCKATVNRRPLQLIYSEKIDSLDEARKREKYFKTASGRR 73
Cdd:pfam01541  1 KGGIYIIRNKDNKLLYVGSTKNLERRLNQHnagKGAKYTRGKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPN 75
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 4-67 1.95e-10

GIY-YIG nuclease superfamily protein; Validated


Pssm-ID: 178979  Cd Length: 86  Bit Score: 51.85  E-value: 1.95e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083736607  4 YIYiLLSLKDYKTYTGSTDNLEKRLKEHHNGK-CKATVNRRPLQLIYSEKIDSLDEARKREKYFK 67
Cdd:PRK00329   8 FLY-LLRCADGSLYTGITTDVERRFAQHQSGKgAKYTRGRPPLTLVFVEPVGDRSEALRAEYRFK 71
GIYc smart00465
GIY-YIG type nucleases (URI domain);
2-51 5.83e-05

GIY-YIG type nucleases (URI domain);


Pssm-ID: 214677 [Multi-domain]  Cd Length: 84  Bit Score: 37.79  E-value: 5.83e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1083736607   2 KGYIYILLSLKDYKTYTGSTDNLEKRLKEHHNGKckaTVNRRPLQLIYSE 51
Cdd:smart00465  1 KPGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGS---RKGRLLIDALLKY 47
 
Name Accession Description Interval E-value
YhbQ COG2827
Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair];
1-81 8.27e-21

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


Pssm-ID: 442075 [Multi-domain]  Cd Length: 82  Bit Score: 77.86  E-value: 8.27e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083736607  1 MKGYIYILLSLKDYKTYTGSTDNLEKRLKEHHNGKC-KATVNRRPLQLIYSEKIDSLDEARKREKYFKTASGRRALKKIF 79
Cdd:COG2827    1 MMYYVYILRCADNGTLYTGVTNDLERRLAEHNSGKGaKFTRKRRPVKLVYYEEFEDRSEALKREKQIKKWSRAKKEALIE 80


                 ..
gi 1083736607 80 ED 81
Cdd:COG2827   81 GD 82
GIY-YIG_SLX1_like cd10449
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 4-70 8.78e-19

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: 72.24  E-value: 8.78e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1083736607  4 YIYILLSLKDYKTYTGSTDNLEKRLKEHHNGKCKATVNRRPLQLIYSEKIDSLDEARKREKYFKTAS 70
Cdd:cd10449    1 YVYILYSEKLDRYYIGYTSDLERRLEQHNSGKSKFTSKYRPWELVYSEAFESKSEALKREKYLKSGK 67
GIY-YIG_UPF0213 cd10456
The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific ...
 4-67 3.14e-17

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: 68.59  E-value: 3.14e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083736607  4 YIYILLSlKDYKTYTGSTDNLEKRLKEHHNGK-CKATVNRRPLQLIYSEKIDSLDEARKREKYFK 67
Cdd:cd10456    2 YVYILRC-ADGSLYTGITTDLERRLAEHNSGKgAKYTRGRRPVKLVYSEEFDDRSEALKREYRIK 65
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 2-73 1.34e-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: 54.65  E-value: 1.34e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083736607  2 KGYIYILLSLKDYKTYTGSTDNLEKRLKEH---HNGKCKATVNRRPLQLIYSEKIDSLDEARKREKYFKTASGRR 73
Cdd:pfam01541  1 KGGIYIIRNKDNKLLYVGSTKNLERRLNQHnagKGAKYTRGKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPN 75
PRK00329 PRK00329
GIY-YIG nuclease superfamily protein; Validated
 4-67 1.95e-10

GIY-YIG nuclease superfamily protein; Validated


Pssm-ID: 178979  Cd Length: 86  Bit Score: 51.85  E-value: 1.95e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083736607  4 YIYiLLSLKDYKTYTGSTDNLEKRLKEHHNGK-CKATVNRRPLQLIYSEKIDSLDEARKREKYFK 67
Cdd:PRK00329   8 FLY-LLRCADGSLYTGITTDVERRFAQHQSGKgAKYTRGRPPLTLVFVEPVGDRSEALRAEYRFK 71
GIY-YIG_unchar_3 cd10448
GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; The family includes ...
 3-78 2.60e-10

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: 51.34  E-value: 2.60e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1083736607  3 GYIYILLSLKDYKTYTGSTDNLEKRLKEHHNGKCKA-TVNRRPLQLIYSEKIDSLDEARKREKYFKtaSGRRAlKKI 78
Cdd:cd10448    1 YYVYILANKRNGTLYIGVTSDLIRRIYEHKEGLGSGfTSKYNVTRLVYYEEFEDIEEAIAREKQLK--KWRRA-WKI 74
GIY-YIG_SF cd00719
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ...
 4-69 1.86e-05

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: 38.50  E-value: 1.86e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083736607  4 YIYILLSLKDYKTYTGSTDNLEKRLKEHHNGKCKATVNR-RPLQLIY-SEKIDSLDEARKREKYFKTA 69
Cdd:cd00719    1 GVYVLYDEDNGLIYVGQTKNLRNRIKEHLRKQRSDWTKGlKPFEILYlEVAPEAESELLDLEAALIKK 68
GIYc smart00465
GIY-YIG type nucleases (URI domain);
2-51 5.83e-05

GIY-YIG type nucleases (URI domain);


Pssm-ID: 214677 [Multi-domain]  Cd Length: 84  Bit Score: 37.79  E-value: 5.83e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1083736607   2 KGYIYILLSLKDYKTYTGSTDNLEKRLKEHHNGKckaTVNRRPLQLIYSE 51
Cdd:smart00465  1 KPGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGS---RKGRLLIDALLKY 47
GIY-YIG_SLX1 cd10455
Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its ...
 4-48 1.89e-04

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: 36.06  E-value: 1.89e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 1083736607  4 YIYILLSLKD---YKTYTGSTDNLEKRLKEhHNGKC----KATVNRRPLQLI 48
Cdd:cd10455    3 GVYLLRSLNPkykGRTYIGFTVNPPRRLRQ-HNGELkggaKKTSRKRPWEMV 53
GIY-YIG_COG3410 cd10439
GIY-YIG domain of uncharacterized bacterial protein structurally related to COG3410; This ...
 5-54 2.65e-03

GIY-YIG domain of uncharacterized bacterial protein structurally related to COG3410; This family contains a group of uncharacterized bacterial proteins. Although their function roles have not been recognized, these proteins contain a putative GIY-YIG domain in their N-terminus. Moreover, a conserved domain COG3410 with unknown function has been found in the C-terminus of most family members.


Pssm-ID: 198386  Cd Length: 80  Bit Score: 33.37  E-value: 2.65e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 1083736607  5 IYILLSLKDYKTYTGSTDNLEKRLKEHHNG---KCKATVNRrpLQLIYSEKID 54
Cdd:cd10439    5 VYILYDKKKKKVYIGETNNILRRLKQHLKDpekKFLRDLNQ--VIVIGHELFN 55
GIY-YIG_MSH cd10438
Catalytic GIY-YIG domain of eukaryotic DNA mismatch repair protein MutS homologs; This family ...
 5-31 5.17e-03

Catalytic GIY-YIG domain of eukaryotic DNA mismatch repair protein MutS homologs; This family represents a putative GIY-YIG nuclease domain C-terminally fused to the DNA-repair ATPase on a small group of eukaryotic DNA mismatch repair protein mutS homologs (MSH). The MSH proteins in this family do not have the zinc finger domain, but have a predicted mitochondrial localization. They might play roles in the recognition and repair of errors made during the replication of DNA. The prototype of this family is the protein encoded by the chloroplast mutator (CHM) locus from Arabidopsis thaliana. It is suggested that this protein could be involved in the maintenance of mitochondrial genome stability.


Pssm-ID: 198385  Cd Length: 72  Bit Score: 32.45  E-value: 5.17e-03
                         10        20
                 ....*....|....*....|....*..
gi 1083736607  5 IYILlSLKDYKTYTGSTDNLEKRLKEH 31
Cdd:cd10438    3 VYIL-RRGDGEYYVGETDNLSGRLEQH 28
 
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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