Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
26  structures 8341  species 0  interactions 18595  sequences 187  architectures

Family: GIY-YIG (PF01541)

Summary: GIY-YIG catalytic domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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

Internal database links

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.

Domain organisation

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

Loading domain graphics...

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 7 members:

DUF123 GIY-YIG GIY_YIG_domain MUG113 RE_Eco29kI SegE_GIY-YIG T5orf172


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes UniProt

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes UniProt
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_489 (release 4.0)
Previous IDs: Exci_endo_N;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bashton M , Bateman A
Number in seed: 35
Number in full: 18595
Average length of the domain: 77.80 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 20.05 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -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: 26
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

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


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


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 26 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 sequence.

Loading structure mapping...