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55  structures 2644  species 2  interactions 4493  sequences 22  architectures

Family: FAD_binding_7 (PF03441)

Summary: FAD binding domain of DNA photolyase

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This is the Wikipedia entry entitled "Photolyase". More...

Photolyase Edit Wikipedia article

FAD binding domain of DNA photolyase
Photolyase 1qnf.png
A deazaflavin photolyase from Anacystis nidulans, illustrating the two light-harvesting cofactors: FADH- (yellow) and 8-HDF (cyan).
Identifiers
Symbol FAD_binding_7
Pfam PF03441
InterPro IPR005101
PROSITE PDOC00331
SCOP 1qnf
SUPERFAMILY 1qnf

Photolyases (EC 4.1.99.3) are DNA repair enzymes that repair damage caused by exposure to ultraviolet light. This enzyme mechanism[1] requires visible light, preferentially from the violet/blue end of the spectrum, and is known as photoreactivation.

Photolyase is a phylogenetically old enzyme which is present and functional in many species, from the bacteria to the fungi to plants and to the animals.[2] Photolyase is particularly important in repairing UV induced damage in plants. However it is no longer working in humans and other placental mammals who instead rely on the less efficient nucleotide excision repair mechanism.[3]

Photolyases bind complementary DNA strands and break certain types of pyrimidine dimers that arise when a pair of thymine or cytosine bases on the same strand of DNA become covalently linked. These dimers result in a 'bulge' of the DNA structure, referred to as a lesion. The more common covalent linkage involves the formation of a cyclobutane bridge. Photolyases have a high affinity for these lesions and reversibly bind and convert them back to the original bases.

A UV radiation induced uracil-uracil cyclobutane dimer (right) is the type of DNA damage which is repaired by DNA photolyase. Note: The above diagram is incorrectly labelled as thymine as the structures lack 5-methyl groups.

Photolyases are flavoproteins and contain two light-harvesting cofactors. All photolyases contain the two-electron-reduced FADH-; they are divided into two main classes based on the second cofactor, which may be either the pterin methenyltetrahydrofolate (MTHF) in folate photolyases or the deazaflavin 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF) in deazaflavin photolyases. Although only FAD is required for catalytic activity, the second cofactor significantly accelerates reaction rate in low-light conditions. The enzyme acts by electron transfer in which the reduced flavin FADH- is activated by light energy and acts as an electron donor to break the pyrimidine dimer.[4]

On the basis of sequence similarities DNA photolyases can be grouped into two classes. The first class contains enzymes from Gram-negative and Gram-positive bacteria, the halophilic archaebacteria Halobacterium halobium, fungi and plants. Proteins containing this domain also include Arabidopsis thaliana cryptochromes 1 and 2, which are blue light photoreceptors that mediate blue light-induced gene expression and modulation of circadian rhythms.

Some sunscreens include photolyase in their ingredients, claiming a reparative action on UV-damaged skin.[5]

Human proteins containing this domain[edit]

CRY1; CRY2;

References[edit]

  1. ^ V. Thiagarajan, M. Byrdin, A.P.M. Eker, P. Müller & K. Brettel (2011). "Kinetics of cyclobutane thymine dimer splitting by DNA photolyase directly monitored in the UV". Proc. Natl. Acad. Sci. USA 108: 9402–9407. doi:10.1073/pnas.1101026108. 
  2. ^ Selby, Christopher P.; Sancar, Aziz (21 November 2006). "A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity". Proceedings of the National Academy of Sciences of the United States of America 103 (47): 17696–700. doi:10.1073/pnas.0607993103. PMC 1621107. PMID 17062752. 
  3. ^ Michael Lynch, José Ignacio Lucas-Lledó; Lynch, M. (19 February 2009). "Evolution of Mutation Rates: Phylogenomic Analysis of the Photolyase/Cryptochrome Family". Molecular Biology and Evolution 26 (5): 1143–1153. doi:10.1093/molbev/msp029. PMC 2668831. PMID 19228922. 
  4. ^ Sancar, A. (2003). "Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors". Chem Rev 103 (6): 2203–37. doi:10.1021/cr0204348. PMID 12797829. 
  5. ^ Kulms, Dagmar; Pöppelmann, Birgit; Yarosh, Daniel; Luger, Thomas A.; Krutmann, Jean; Schwarz, Thomas (1999). "Nuclear and cell membrane effects contribute independently to the induction of apoptosis in human cells exposed to UVB radiation". PNAS 96 (14): 7974–7979. doi:10.1073/pnas.96.14.7974. PMC 22172. PMID 10393932. 

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FAD binding domain of DNA photolyase Provide feedback

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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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005101

This entry represents a multi-helical domain composed of two all-alpha subdomains that is found as the C-terminal domain in cryptochrome proteins, as well as at the N-terminal of DNA photolyase where it acts as a FAD-binding domain (the N-terminal of DNA photolyase binds a light-harvesting cofactor).

Photolyases and cryptochromes are related flavoproteins that bind FAD. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes (CRY1 and CRY2) are blue light photoreceptors that mediate blue light-induced gene expression [PUBMED:12535521, PUBMED:15299148].

DNA photolyases are DNA repair enzymes that repair mismatched pyrimidine dimers induced by exposure to ultra-violet light. They bind to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), they catalyse dimer splitting, breaking the cyclobutane ring joining the two pyrimidines of the dimer so as to split them into the constituent monomers; this process is called photoreactivation. DNA photolyases require two choromophore-cofactors for their activity. All monomers contain a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm [PUBMED:7604260, PUBMED:15213381].

Gene Ontology

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Domain organisation

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Alignments

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(163)
Full
(4493)
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(3950)
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(7444)
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(488)
RP35
(923)
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(1231)
RP75
(1440)
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  Seed
(163)
Full
(4493)
Representative proteomes NCBI
(3950)
Meta
(7444)
RP15
(488)
RP35
(923)
RP55
(1231)
RP75
(1440)
Alignment:
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  Seed
(163)
Full
(4493)
Representative proteomes NCBI
(3950)
Meta
(7444)
RP15
(488)
RP35
(923)
RP55
(1231)
RP75
(1440)
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

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Curation and family details

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Seed source: SCOP
Previous IDs: none
Type: Domain
Author: Griffiths-Jones SR
Number in seed: 163
Number in full: 4493
Average length of the domain: 245.00 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 51.07 %

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 20.1 20.1
Trusted cut-off 20.1 20.1
Noise cut-off 19.4 19.9
Model length: 277
Family (HMM) version: 9
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Species distribution

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Interactions

There are 2 interactions for this family. More...

FAD_binding_7 DNA_photolyase

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 FAD_binding_7 domain has been found. There are 55 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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