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20  structures 19537  species 1  interaction 38331  sequences 123  architectures

Family: GIY-YIG (PF01541)

Summary: GIY-YIG catalytic domain

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GIY-YIG catalytic domain Provide feedback

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 [4]. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.

Literature references

  1. Sharma M, Ellis RL, Hinton DM; , Proc Natl Acad Sci U S A 1992;89:6658-6662.: Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage. PUBMED:1631169 EPMC:1631169

  2. Aravind L, Walker DR, Koonin EV; , Nucleic Acids Res 1999;27:1223-1242.: Conserved domains in DNA repair proteins and evolution of repair systems. PUBMED:9973609 EPMC:9973609

  3. Kowalski JC, Belfort M, Stapleton MA, Holpert M, Dansereau JT, Pietrokovski S, Baxter SM, Derbyshire V; , Nucleic Acids Res 1999;27:2115-2125.: Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings. PUBMED:10219084 EPMC:10219084

  4. Van Roey P, Meehan L, Kowalski JC, Belfort M, Derbyshire V; , Nat Struct Biol 2002;9:806-811.: Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. PUBMED:12379841 EPMC:12379841

  5. Dunin-Horkawicz S, Feder M, Bujnicki JM; , BMC Genomics. 2006;7:98.: Phylogenomic analysis of the GIY-YIG nuclease superfamily. PUBMED:16646971 EPMC:16646971

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000305

Nucleases of the GIY-YIG family are involved in many cellular processes, including DNA repair and recombination, transfer of mobile genetic elements, and restriction of incoming foreign DNA. The GIY-YIG superfamily groups together nucleases characterised by the presence of a domain of typically ~100 amino acids, with two short motifs "GIY" and "YIG" in the N-terminal part, followed by an Arg residue in the centre and a Glu residue in the C-terminal part [PUBMED:10219084, PUBMED:12379841, PUBMED:15692561, PUBMED:16646971, PUBMED:19361436].

The GIY-YIG domain forms a compact structural domain, which serves as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. The GIY-YIG domain has an alpha/bera-sandwich architecture with a central three-stranded antiparallel beta-sheet flanked by three-helices. The three-stranded anti-parallel beta-sheet contains the GIY-YIG sequence elements. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site [PUBMED:12379841, PUBMED:15692561, PUBMED:16646971, PUBMED:19361436].

The GIY-YIG domain has been implicated in a variety of cellular processes involving DNA cleavage, from self-propagation with or without introns, to restriction of foreign DNA, to DNA repair and maintenance of genome stability [PUBMED:16646971].

Some proteins known to contain a GIY-YIG domain include:

  • Eukaryotic Slx-1 proteins, involved in the maintenance of the rDNA copy number. They have a C-terminal RING finger Zn-binding domain.
  • Mamalian ankyrin repeat and LEM domain- containing protein 1 (ANKLE1).
  • Bacterial and archaeal UvrC subunits of (A)BC excinucleases, which remove damaged nucleotides by incising the damaged strand on both sides of the lesion. Paramecium bursaria Chlorella virus 1 (pbvc1).
  • Phage T4 endonucleases SegA to E, probably involved in the movement of the endonuclease-encoding DNA.
  • Phage T4 intron-associated endonuclease 1 (I-TevI), specific to the thymidylate synthase (td) gene splice junction and involved in intron homing.

This entry represents GIY-YIG nuclease superfamily, and identifies the GIY-YIG domain in diverse and distantly related superfamily members, such as Slx1 [PUBMED:16646971].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan GIY-YIG (CL0418), which has the following description:

Based on the analysis of genomic distribution, patterns of domain fusions and phylogenetic considerations for individual families, an evolutionary scenario is proposed that explains the emergence and development of the major branches of the GIY-YIG superfamily that links the Slx-type with the UvrC-like endonucleases. Most families appear to target DNA. The GIY-YIG domain has been quite successful in forming monomeric nucleases that utilise additional domains to recognise its DNA targets; this collection of domains can range from extremely simple DNA-binding elements (as in the case of I-TevI) to modules with independent enzymatic activities (as in the case of UvrC or the Penelope elements) [1].

The clan contains the following 4 members:

DUF123 GIY-YIG MUG113 T5orf172


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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_489 (release 4.0)
Previous IDs: Exci_endo_N;
Type: Domain
Author: Bashton M, Bateman A
Number in seed: 39
Number in full: 38331
Average length of the domain: 76.70 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 19.50 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.6 22.6
Trusted cut-off 22.6 22.6
Noise cut-off 22.5 22.5
Model length: 78
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the GIY-YIG domain has been found. There are 20 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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