Any feedback?
Literature summary for 4.1.99.3 extracted from
- Photolyase dynamics and electron-transfer mechanisms of DNA repair (2017), Arch. Biochem. Biophys., 632, 158-174 .
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) | Arabidopsis thaliana | - |
2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | Methanosarcina mazei | - |
2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | Synechococcus elongatus PCC 7942 = FACHB-805 | - |
2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | Caulobacter vibrioides | - |
2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | Synechococcus elongatus PCC 7942 = FACHB-805 ATCC 27144 / PCC 6301 / SAUG 1402/1 | - |
2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | Caulobacter vibrioides NA1000/CB15N | - |
2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | Methanosarcina mazei ATCC BAA-159 | - |
2 pyrimidine residues (in DNA) | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Arabidopsis thaliana | Q84KJ5 | - |
- |
| Arabidopsis thaliana | Q9SB00 | - |
- |
| Caulobacter vibrioides | A0A0H3C7H5 | i.e. Caulobacter ribroides | - |
| Caulobacter vibrioides NA1000/CB15N | A0A0H3C7H5 | i.e. Caulobacter ribroides | - |
| Escherichia coli | P00914 | - |
- |
| Methanosarcina mazei | Q8PYK9 | - |
- |
| Methanosarcina mazei ATCC BAA-159 | Q8PYK9 | - |
- |
| Synechococcus elongatus PCC 7942 = FACHB-805 | P05327 | - |
- |
| Synechococcus elongatus PCC 7942 = FACHB-805 ATCC 27144 / PCC 6301 / SAUG 1402/1 | P05327 | - |
- |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) | the repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. Repair photocycle of the PLs and development of a unified repair mechanism for all CPD PLs with the critical, bifurcating electron transfer pathways through the folded flavin cofactor in the conserved active site structure, overview | Escherichia coli | |
| cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) | the repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. Repair photocycle of the PLs and development of a unified repair mechanism for all CPD PLs with the critical, bifurcating electron transfer pathways through the folded flavin cofactor in the conserved active site structure, overview | Arabidopsis thaliana | |
| cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) | the repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. Repair photocycle of the PLs and development of a unified repair mechanism for all CPD PLs with the critical, bifurcating electron transfer pathways through the folded flavin cofactor in the conserved active site structure, overview | Methanosarcina mazei | |
| cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) | the repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. Repair photocycle of the PLs and development of a unified repair mechanism for all CPD PLs with the critical, bifurcating electron transfer pathways through the folded flavin cofactor in the conserved active site structure, overview | Synechococcus elongatus PCC 7942 = FACHB-805 | |
| cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) | the repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. Repair photocycle of the PLs and development of a unified repair mechanism for all CPD PLs with the critical, bifurcating electron transfer pathways through the folded flavin cofactor in the conserved active site structure, overview | Caulobacter vibrioides |
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) | - |
Arabidopsis thaliana | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | - |
Methanosarcina mazei | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | - |
Synechococcus elongatus PCC 7942 = FACHB-805 | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | - |
Caulobacter vibrioides | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | - |
Synechococcus elongatus PCC 7942 = FACHB-805 ATCC 27144 / PCC 6301 / SAUG 1402/1 | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | - |
Caulobacter vibrioides NA1000/CB15N | 2 pyrimidine residues (in DNA) | - |
? | |
| cyclobutadipyrimidine (in DNA) | - |
Methanosarcina mazei ATCC BAA-159 | 2 pyrimidine residues (in DNA) | - |
? | |
| additional information | enzyme-substrate complex structure of class II PL from Methanosarcina mazei (MmPL) | Methanosarcina mazei | ? | - |
? | |
| additional information | enzyme-substrate complex structure of class II PL from Methanosarcina mazei (MmPL) | Methanosarcina mazei ATCC BAA-159 | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| More | enzyme-substrate complex structure of class II PL from Methanosarcina mazei (MmPL) | Methanosarcina mazei |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| AnPL | - |
Synechococcus elongatus PCC 7942 = FACHB-805 |
| AtPL | - |
Arabidopsis thaliana |
| CcPL | - |
Caulobacter vibrioides |
| class I PL | - |
Escherichia coli |
| class I PL | - |
Synechococcus elongatus PCC 7942 = FACHB-805 |
| class II AtPL | - |
Arabidopsis thaliana |
| class II PL | - |
Methanosarcina mazei |
| class III PL | - |
Caulobacter vibrioides |
| CRYD | - |
Arabidopsis thaliana |
| cryptochrome-3 | - |
Arabidopsis thaliana |
| EcPL | - |
Escherichia coli |
| MmPL | - |
Methanosarcina mazei |
| PHR1 | - |
Arabidopsis thaliana |
| ssDNA AtCRY3 | - |
Arabidopsis thaliana |
| ssDNA PL | - |
Arabidopsis thaliana |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| FAD | dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state | Arabidopsis thaliana | |
| FAD | dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state | Methanosarcina mazei | |
| FAD | dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state | Synechococcus elongatus PCC 7942 = FACHB-805 | |
| FAD | dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state | Caulobacter vibrioides | |
| FAD | dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state. Using femtosecond (fs)-resolved spectroscopy and site-directed mutagenesis, the dynamics of class I PL from Escherichia coli (EcPL) in four redox states are investigated | Escherichia coli | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the enzyme belongs to the enzyme superfamily of photolyase/cryptochromes. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. The unified, bifurcated electron transfer mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. Classes of photolyases and structures of CPD and 6-4 photolyases, overview. The diverse subfamily of CPD photolyases consists of classes I, II and III, and ssDNA PLs | Escherichia coli |
| evolution | the enzyme belongs to the enzyme superfamily of photolyase/cryptochromes. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. The unified, bifurcated electron transfer mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. Classes of photolyases and structures of CPD and 6-4 photolyases, overview. The diverse subfamily of CPD photolyases consists of classes I, II and III, and ssDNA PLs | Arabidopsis thaliana |
| evolution | the enzyme belongs to the enzyme superfamily of photolyase/cryptochromes. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. The unified, bifurcated electron transfer mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. Classes of photolyases and structures of CPD and 6-4 photolyases, overview. The diverse subfamily of CPD photolyases consists of classes I, II and III, and ssDNA PLs | Methanosarcina mazei |
| evolution | the enzyme belongs to the enzyme superfamily of photolyase/cryptochromes. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. The unified, bifurcated electron transfer mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. Classes of photolyases and structures of CPD and 6-4 photolyases, overview. The diverse subfamily of CPD photolyases consists of classes I, II and III, and ssDNA PLs | Synechococcus elongatus PCC 7942 = FACHB-805 |
| evolution | the enzyme belongs to the enzyme superfamily of photolyase/cryptochromes. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. The unified, bifurcated electron transfer mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. Classes of photolyases and structures of CPD and 6-4 photolyases, overview. The diverse subfamily of CPD photolyases consists of classes I, II and III, and ssDNA PLs | Caulobacter vibrioides |
| additional information | in class I EcPL, the initial electron injection adopts dominant tunneling pathways directly from LfH- to CPD. Reaction free energy profile along the reaction coordinate for EcPL CPD repair, overview | Escherichia coli |
| additional information | the crystal structure of Anacystis nidulans photolyase with CPD complex shows that the Ade moiety of FADH- is at van der Waals distances with both base moieties of CPD, 3.1 A to the 5' side and 3.2 A to 3'. The first carbon atom is linked to the isoalloxazine ring at 3.6 A | Synechococcus elongatus PCC 7942 = FACHB-805 |
| physiological function | CPD photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair | Arabidopsis thaliana |
| physiological function | CPD photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair | Methanosarcina mazei |
| physiological function | CPD photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair | Caulobacter vibrioides |
| physiological function | CPD photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair. Class I photolyase shows electron tunneling and high repair efficiency | Escherichia coli |
| physiological function | CPD photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair. Class I photolyase shows electron tunneling and high repair efficiency | Synechococcus elongatus PCC 7942 = FACHB-805 |
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
