GIYc

GIY-YIG type nucleases (URI domain)

• SMART accession number: SM00465
• Interpro abstract (IPR000305):

  During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products (PUBMED:12034838). The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.

  It 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.

• GO process: DNA repair (GO:0006281)
• GO component: intracellular (GO:0005622)
• GO function: nuclease activity (GO:0004518)

There are 1161 GIYc domains in 1161 proteins in SMART's nrdb database.

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Aravind L, Walker DR, Koonin EV
• Conserved domains in DNA repair proteins and evolution of repair systems.
• Nucleic Acids Res. 1999; 27: 1223-42

A detailed analysis of protein domains involved in DNA repair was performed by comparing the sequences of the repair proteins from two well-studied model organisms, the bacterium Escherichia coli and yeast Saccharomyces cerevisiae, to the entire sets of protein sequences encoded in completely sequenced genomes of bacteria, archaea and eukaryotes. Previously uncharacterized conserved domains involved in repair were identified, namely four families of nucleases and a family of eukaryotic repair proteins related to the proliferating cell nuclear antigen. In addition, a number of previously undetected occurrences of known conserved domains were detected; for example, a modified helix-hairpin-helix nucleic acid-binding domain in archaeal and eukaryotic RecA homologs. There is a limited repertoire of conserved domains, primarily ATPases and nucleases, nucleic acid-binding domains and adaptor (protein-protein interaction) domains that comprise the repair machinery in all cells, but very few of the repair proteins are represented by orthologs with conserved domain architecture across the three superkingdoms of life. Both the external environment of an organism and the internal environment of the cell, such as the chromatin superstructure in eukaryotes, seem to have a profound effect on the layout of the repair systems. Another factor that apparently has made a major contribution to the composition of the repair machinery is horizontal gene transfer, particularly the invasion of eukaryotic genomes by organellar genes, but also a number of likely transfer events between bacteria and archaea. Several additional general trends in the evolution of repair proteins were noticed; in particular, multiple, independent fusions of helicase and nuclease domains, and independent inactivation of enzymatic domains that apparently retain adaptor or regulatory functions.

• Kowalski JC et al.
• Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings.
• Nucleic Acids Res. 1999; 27: 2115-25

I-TevI is a member of the GIY-YIG family of homing endonucleases. It is folded into two structural and functional domains, an N-terminal catalytic domain and a C-terminal DNA-binding domain, separated by a flexible linker. In this study we have used genetic analyses, computational sequence analysis andNMR spectroscopy to define the configuration of theN-terminal domain and its relationship to the flexible linker. The catalytic domain is an alpha/beta structure contained within the first 92 amino acids of the 245-amino acid protein followed by an unstructured linker. Remarkably, this structured domain corresponds precisely to the GIY-YIG module defined by sequence comparisons of 57 proteins including more than 30 newly reported members of the family. Although much of the unstructured linker is not essential for activity, residues 93-116 are required, raising the possibility that this region may adopt an alternate conformation upon DNA binding. Two invariant residues of the GIY-YIG module, Arg27 and Glu75, located in alpha-helices, have properties of catalytic residues. Furthermore, the GIY-YIG sequence elements for which the module is named form part of a three-stranded antiparallel beta-sheet that is important for I-TevI structure and function.

• Derbyshire V, Kowalski JC, Dansereau JT, Hauer CR, Belfort M
• Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site.
• J Mol Biol. 1997; 265: 494-506

I-TevI, the T4 td intron-encoded endonuclease, catalyzes the first step in intron homing by making a double-strand break in the intronless allele within a sequence designated the homing site. The 28 kDa enzyme, which interacts with the homing site over a span of 37 bp, binds as a monomer, contacting two domains of the substrate. In this study, limited proteolysis experiments indicate that I-TevI consists of two domains that behave as discrete physical entities as judged by a number of functional and structural criteria. Overexpression clones for each domain were constructed and the proteins were purified. The carboxy-terminal domain has DNA-binding activity coincident with the primary binding region of the homing site and binds with the same affinity as the full-length enzyme. The isolated amino-terminal domain, contains the conserved GIY-YIG motif, consistent with its being the catalytic domain. Furthermore, site-directed mutagenesis of a conserved arginine residue within the extended motif rendered the full-length protein catalytically inactive, although DNA-binding was maintained. This is the first evidence that the GIY-YIG motif is important for catalytic activity. An enzyme with an N-terminal catalytic domain and a C-terminal DNA-binding domain connected by a flexible linker is in accord with the bipartite structure of the homing site.

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
100.00	map03030	DNA replication

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with GIYc domain which could be assigned to a KEGG orthologous group, and not all proteins containing GIYc domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

Structure (3D structures containing this domain)

3D Structures of GIYc domains in PDB

PDB code	Title
1ln0	Structure of the catalytic domain of homing endonuclease i- tevi
1mk0	Catalytic domain of intron endonuclease i-tevi, e75a mutant
1ycz	Crystal structure of the giy-yig n-terminal endonuclease domain of uvrc from thermotoga maritima
1yd0	Crystal structure of the giy-yig n-terminal endonuclease domain of uvrc from thermotoga maritima bound to its catalytic divalent cation: manganese
1yd1	Crystal structure of the giy-yig n-terminal endonuclease domain of uvrc from thermotoga maritima bound to its catalytic divalent cation: magnesium
1yd2	Crystal structure of the giy-yig n-terminal endonuclease domain of uvrc from thermotoga maritima: point mutant y19f bound to the catalytic divalent cation
1yd3	Crystal structure of the giy-yig n-terminal endonuclease domain of uvrc from thermotoga maritima: point mutant y43f bound to its catalytic divalent cation
1yd4	Crystal structure of the giy-yig n-terminal endonuclease domain of uvrc from thermotoga maritima: point mutant y29f bound to its catalytic divalent cation
1yd5	Crystal structure of the giy-yig n-terminal endonuclease domain of uvrc from thermotoga maritima: point mutant n88a bound to its catalytic divalent cation
1yd6	Crystal structure of the giy-yig n-terminal endonuclease domain of uvrc from bacillus caldotenax
1ywl	Solution nmr structure of the protein ef2693 from e. faecalis: northeast structural genomics consortium target efr36
1zg2	Solution nmr structure of the upf0213 protein bh0048 from bacillus halodurans. northeast structural genomics target bhr2.

Links (links to other resources describing this domain)

• PFAM: Exci_endo_N
• INTERPRO: IPR000305