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71  structures 12328  species 3  interactions 14854  sequences 36  architectures

Family: DNA_photolyase (PF00875)

Summary: DNA photolyase

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

This is the Wikipedia entry entitled "DNA photolyase". More...

DNA photolyase Edit Wikipedia article

DNA photolyase may refer to:

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

DNA photolyase Provide feedback

This domain binds a light harvesting cofactor.

Literature references

  1. Tamada T, Kitadokoro K, Higuchi Y, Inaka K, Yasui A, de Ruiter PE, Eker AP, Miki K , Nat Struct Biol 1997;4:887-891.: Crystal structure of DNA photolyase from Anacystis nidulans. PUBMED:9360600 EPMC:9360600


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006050

The photolyase/cryptochrome family consists of flavoproteins that perform various functions using blue-light photons as an energie source. It is present in all three domains of life, that is, archaea, eubacteria, and eukaryotes, and hence has arisen very early during evolution to protect genomes against the genotoxic effects of ultraviolet light originating from the sun. The photolyase/cryptochrome family is divided into two major groups: photolyases and cryptochromes. Photolyases repair cytotoxic and mutagenic UV-induced photolesions in DNA in many species from bacteria to plants and animals by using a light-dependent repair mechanism. It involves light absorption, electron transfer from an excited reduced and deprotanated FADH(-) to the flipped-out photolesion, followed by the fragmentation of the photolesions. Cryptochromes are highly related proteins that generally no longer repair damaged DNA, but function as photoreceptors. Cryptochromes regulate growth and development in plants and the circadian clock in animals [PUBMED:12535521, PUBMED:19074258, PUBMED:9487120, PUBMED:19570997, PUBMED:21892138, PUBMED:22170053, PUBMED:22325881].

Both photolyases and cryptochromes have a bilobal architecture consisting of two domains: an N-terminal alpha/beta domain that may contain a light- harvesting chromophore to additionally broaden their activity spectra and a C- terminal alpha-helical catalytic domain comprising the light-sensitive FAD cofactor. Diverse classes of antenna chromophores likes 5,10- methenyltetrahydrofolate (MTHF), 8-hydroxydeazaflavin, FMN or FAD have been identified in some photolyase/cryptochrome to broaden their activity spectra, whereas many others apparently lack any bound antenna chromophores.

This entry represents the photolyase/cryptochrome alpha/beta domain. It adopts a dinucleotide binding fold with a five-stranded parallel beta sheet flanked on both sides by alpha helices [PUBMED:12535521, PUBMED:21892138].

Domain organisation

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

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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
(88)
Full
(14854)
Representative proteomes NCBI
(8584)
Meta
(3006)
RP15
(454)
RP35
(1087)
RP55
(1577)
RP75
(1960)
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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
(88)
Full
(14854)
Representative proteomes NCBI
(8584)
Meta
(3006)
RP15
(454)
RP35
(1087)
RP55
(1577)
RP75
(1960)
Alignment:
Format:
Order:
Sequence:
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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
(88)
Full
(14854)
Representative proteomes NCBI
(8584)
Meta
(3006)
RP15
(454)
RP35
(1087)
RP55
(1577)
RP75
(1960)
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.

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_777 (release 3.0)
Previous IDs: none
Type: Domain
Author: Bateman A, Griffiths-Jones SR
Number in seed: 88
Number in full: 14854
Average length of the domain: 165.40 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 34.76 %

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 26.3 26.3
Trusted cut-off 26.4 26.3
Noise cut-off 26.2 26.2
Model length: 164
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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

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Interactions

There are 3 interactions for this family. More...

DNA_photolyase FAD_binding_7 FAD_binding_7

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 DNA_photolyase domain has been found. There are 71 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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