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20  structures 4836  species 1  interaction 9798  sequences 83  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

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 domain 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.

The homology region 1 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.

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

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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.

  Seed
(105)
Full
(9798)
Representative proteomes NCBI
(7330)
Meta
(3586)
RP15
(771)
RP35
(1529)
RP55
(1995)
RP75
(2329)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(105)
Full
(9798)
Representative proteomes NCBI
(7330)
Meta
(3586)
RP15
(771)
RP35
(1529)
RP55
(1995)
RP75
(2329)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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.

  Seed
(105)
Full
(9798)
Representative proteomes NCBI
(7330)
Meta
(3586)
RP15
(771)
RP35
(1529)
RP55
(1995)
RP75
(2329)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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...

Trees

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
Author: Bashton M, Bateman A
Number in seed: 105
Number in full: 9798
Average length of the domain: 77.80 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 19.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -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: 80
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

GIY-YIG

Structures

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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