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Literature summary for 4.1.99.3 extracted from
- The photolyase/cryptochrome family of proteins as DNA repair enzymes and transcriptional repressors (2017), Photochem. Photobiol., 93, 93-103 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| DNA and amino acid sequence determination and analysis, seven genes displaying homology to the CPF in Cyanidioschyzon merolae, an extremophilic microalga. Characterization of these seven putative CPF members identifies three genes encoding CRY-DASHs, accordingly named as CmPHR2, CmPHR5 and CmPHR6 | Cyanidioschyzon merolae |
| unrooted phylogenetic tree | Escherichia coli |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| crystal structure analysis, structure comparisons, overview | Escherichia coli |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| W306F | naturally occuring mutant | Escherichia coli |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| cyclobutadipyrimidine (in DNA) | Escherichia coli | - |
2 pyrimidine residues (in DNA) | - |
? |  |
| cyclobutadipyrimidine (in DNA) | Vibrio cholerae serotype O1 | - |
2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | Cyanidioschyzon merolae | - |
2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 | - |
2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | Cyanidioschyzon merolae 10D | - |
2 pyrimidine residues (in DNA) | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Cyanidioschyzon merolae | M1V3I5 | - |
- |
| Cyanidioschyzon merolae 10D | M1V3I5 | - |
- |
| Escherichia coli | P00914 | - |
- |
| Vibrio cholerae serotype O1 | Q9KNA8 | - |
- |
| Vibrio cholerae serotype O1 | Q9KR33 | - |
- |
| Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 | Q9KNA8 | - |
- |
| Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 | Q9KR33 | - |
- |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) | reaction mechanisms of CPD DNA photolyase and cytochrome DASH, detailed overview | Vibrio cholerae serotype O1 | |
| cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) | reaction mechanisms of CPD DNA photolyase and cytochrome DASH, detailed overview | Cyanidioschyzon merolae | |
| cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) | reaction mechanisms of CPD DNA photolyase and cytochrome DASH, detailed overview. Proposed intraprotein electron transfer from W306 to FADH radical is not a part of the normal photolyase photocycle in vivo | Escherichia coli |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| cyclobutadipyrimidine (in DNA) | - |
Escherichia coli | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | - |
Vibrio cholerae serotype O1 | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | - |
Cyanidioschyzon merolae | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | the pyrimidine dimer is flipped out from the DNA helix into the central cavity, thereby coming within van der Waals contact distance of the FAD molecule. This central pocket is lined on one side with hydrophobic residues and with polar residues on the other, thus matching the asymmetric polarity of the thymidine dimer | Escherichia coli | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | the pyrimidine dimer is flipped out from the DNA helix into the central cavity, thereby coming within van der Waals contact distance of the FAD molecule. This central pocket is lined on one side with hydrophobic residues and with polar residues on the other, thus matching the asymmetric polarity of the thymidine dimer | Vibrio cholerae serotype O1 | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | the pyrimidine dimer is flipped out from the DNA helix into the central cavity, thereby coming within van der Waals contact distance of the FAD molecule. This central pocket is lined on one side with hydrophobic residues and with polar residues on the other, thus matching the asymmetric polarity of the thymidine dimer | Cyanidioschyzon merolae | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | - |
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | the pyrimidine dimer is flipped out from the DNA helix into the central cavity, thereby coming within van der Waals contact distance of the FAD molecule. This central pocket is lined on one side with hydrophobic residues and with polar residues on the other, thus matching the asymmetric polarity of the thymidine dimer | Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | - |
Cyanidioschyzon merolae 10D | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | the pyrimidine dimer is flipped out from the DNA helix into the central cavity, thereby coming within van der Waals contact distance of the FAD molecule. This central pocket is lined on one side with hydrophobic residues and with polar residues on the other, thus matching the asymmetric polarity of the thymidine dimer | Cyanidioschyzon merolae 10D | 2 pyrimidine residues (in DNA) | - |
? | |
| additional information | CmPHR2 and CmPHR5 specifically repair ssDNA, while the other CRY-DASH (CmPHR6) repairs neither (6-4) photoproduct nor CPD damage in ssDNA or dsDNA. Comparison of the binding constants for ssDNA and dsDNA of Vibrio cholerae CPD photolyase and CRY-DASH by surface plasmon resonance | Vibrio cholerae serotype O1 | ? | - |
? | |
| additional information | comparison of the binding constants for ssDNA and dsDNA of Vibrio cholerae CPD photolyase and CRY-DASH by surface plasmon resonance | Vibrio cholerae serotype O1 | ? | - |
? | |
| additional information | comparison of the binding constants for ssDNA and dsDNA of Vibrio cholerae CPD photolyase and CRY-DASH by surface plasmon resonance | Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 | ? | - |
? | |
| additional information | CmPHR2 and CmPHR5 specifically repair ssDNA, while the other CRY-DASH (CmPHR6) repairs neither (6-4) photoproduct nor CPD damage in ssDNA or dsDNA. Comparison of the binding constants for ssDNA and dsDNA of Vibrio cholerae CPD photolyase and CRY-DASH by surface plasmon resonance | Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| More | the N-terminal alpha/beta domain is a typical dinucleotide-binding domain with five beta-sheets and five alpha-helices. The C-terminal alpha-helical domain consists of 14 alpha-helices, with structural analysis indicating a cavity at the center where the FAD is found | Escherichia coli |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| CPD photolyase | - |
Escherichia coli |
| CPD photolyase | - |
Vibrio cholerae serotype O1 |
| Cry-DASH | - |
Vibrio cholerae serotype O1 |
| Cry-DASH | - |
Cyanidioschyzon merolae |
| Cry1 | - |
Vibrio cholerae serotype O1 |
| CRYPTOCHROME DASH | - |
Vibrio cholerae serotype O1 |
| CRYPTOCHROME DASH | - |
Cyanidioschyzon merolae |
| CYME_CMA044C | - |
Cyanidioschyzon merolae |
| cytochrome DASH | - |
Vibrio cholerae serotype O1 |
| cytochrome DASH | - |
Cyanidioschyzon merolae |
| DNA photolyase | - |
Cyanidioschyzon merolae |
| phrA | - |
Vibrio cholerae serotype O1 |
| ssDNA photolyase | - |
Vibrio cholerae serotype O1 |
| ssDNA photolyase | - |
Cyanidioschyzon merolae |
| VcCry1 | - |
Vibrio cholerae serotype O1 |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| 5,10-methenyltetrahydrofolate | - |
Vibrio cholerae serotype O1 | |
| 5,10-methenyltetrahydrofolate | - |
Cyanidioschyzon merolae | |
| 5,10-methenyltetrahydrofolate | observed in the cleft between the two domains, where it interacts with two critical amino acid residues, Cys292 and Lys293 | Escherichia coli | |
| FAD | - |
Vibrio cholerae serotype O1 | |
| FAD | - |
Cyanidioschyzon merolae | |
| FAD | bound in a C-terminal alpha-helix cavity, the C-terminal alpha-helical domain consists of 14 alpha-helices. FAD is held in a U-shaped conformation by interaction with 14 conserved amino acid residues | Escherichia coli | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the enzyme belongs to the photolyase/cryptochrome family of proteins, phylogenetic tree of the cryptochrome/photolyase family (CPF), unrooted phylogenetic tree. The cryptochrome/photolyase family (CPF) includes photoreceptors that perform different functions in different organisms. The class of the CPF known as CRY-DASHs is found in algae, bacteria, plants and animals. CRY-DASH proteins have photolyase activity. Because they specifically repair CPD photoproducts in single-stranded DNA (ssDNA) rather than double-stranded DNA (dsDNA), they are designated as ssDNA photolyases | Vibrio cholerae serotype O1 |
| evolution | the enzyme belongs to the photolyase/cryptochrome family of proteins, phylogenetic tree of the cryptochrome/photolyase family (CPF), unrooted phylogenetic tree. The cryptochrome/photolyase family (CPF) includes photoreceptors that perform different functions in different organisms. The class of the CPF known as CRY-DASHs is found in algae, bacteria, plants and animals. CRY-DASH proteins have photolyase activity. Because they specifically repair CPD photoproducts in single-stranded DNA (ssDNA) rather than double-stranded DNA (dsDNA), they are designated as ssDNA photolyases | Cyanidioschyzon merolae |
| evolution | the enzyme belongs to the photolyase/cryptochrome family of proteins, phylogenetic tree of the cryptochrome/photolyase family (CPF), unrooted phylogenetic tree. The cryptochrome/photolyase family (CPF) includes photoreceptors that perform different functions in different organisms. UV is responsible for the formation of two major types of damage-associated photoproducts on DNA: cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts (Pyr [6-4] Pyr). Two different types of photolyases were eventually discovered: CPD and (6-4) photolyases (EC 4.1.99.13). CPD photolyases repair pyrimidine dimers, while (6-4) photolyases repair Pyr[6-4]Pyr photoproducts | Escherichia coli |
| physiological function | CRY-DASH proteins have photolyase activity, photolyases repair Pyr<>Pyr dimers. Photolyases repair ultraviolet-induced DNA damage by a process known as photoreactivation using photons absorbed from the blue end of the light spectrum | Vibrio cholerae serotype O1 |
| physiological function | CRY-DASH proteins have photolyase activity, photolyases repair Pyr<>Pyr dimers. Photolyases repair ultraviolet-induced DNA damage by a process known as photoreactivation using photons absorbed from the blue end of the light spectrum. Consistent with their role in global gene regulation, cryptochrome genes (CmPHR2, CmPHR3 and CmPHR7) are differentially regulated, suggesting that they have a potential role in light-dependent transcriptional regulation in Cyanidioschyzon merolae | Cyanidioschyzon merolae |
| physiological function | UV is responsible for the formation of damage-associated photoproducts on DNA: cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts (Pyr [6-4] Pyr). CPD photolyases repair pyrimidine dimers. Photolyases repair ultraviolet-induced DNA damage by a process known as photoreactivation using photons absorbed from the blue end of the light spectrum | Escherichia coli |
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