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Literature summary extracted from

  • Mueller, M.; Carell, T.
    Structural biology of DNA photolyases and cryptochromes (2009), Curr. Opin. Struct. Biol., 19, 277-285.
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.1.99.3 photolyase-like domain of Cry1 Arabidopsis thaliana
4.1.99.3 shows an N-terminal alpha/beta domain and a C-terminal alpha-helical domain Escherichia coli
4.1.99.3 shows an N-terminal alpha/beta domain and a C-terminal alpha-helical domain. In complex with a DNA-duplex containing a synthetic cyclobutane-pyrimidine-dimers lesion analog, which shows that the protein fold changes only marginally upon DNA binding. CPD-photolyase proteins fully open the DNA-duplex structure at the damaged site and flip the dinucleotide lesion out of the duplex into the active site. Lesion comes in close contact (3 A) with the active FADH-cofactor Synechococcus elongatus PCC 7942 = FACHB-805
4.1.99.13 two crystal structures of the (6-4) photolyase bound to lesion containing DNA before and after repair, repair does not involve oxetane formation before light-induced electron transfer. The histidine 369, supposed to activate the acylimine, is in a position that does not allow efficient proton donation and hence activation of this substructure Drosophila melanogaster

Organism

EC Number Organism UniProt Comment Textmining
4.1.99.3 Arabidopsis thaliana
-
-
-
4.1.99.3 Escherichia coli P00914
-
-
4.1.99.3 Homo sapiens
-
-
-
4.1.99.3 Sulfurisphaera tokodaii
-
-
-
4.1.99.3 Synechococcus elongatus PCC 7942 = FACHB-805
-
-
-
4.1.99.3 Thermus thermophilus P61497
-
-
4.1.99.13 Arabidopsis thaliana O48652
-
-
4.1.99.13 Drosophila melanogaster
-
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.99.3 adenosine 5'-(beta,gamma-imido)triphosphate Cry1 Arabidopsis thaliana ?
-
 ?
4.1.99.3 additional information CPD-photolyase is a DNA repair protein, the electron-transport chain of Cry1 involves a Tyr residue as initial electron donor. For Cry3, weak but unspecific DNA binding, for Cry1, DNA binding cannot be detected. Cry2, whose surface largely resembles that of Cry1, does bind to DNA. Cry3 does repair cyclobutane-pyrimidine-dimers when the lesion is located in a preflipped out state such as in bulges of dsDNA. DASH cryptochromes are single-strand-specific CPD-photolyases Arabidopsis thaliana ?
-
 ?
4.1.99.3 additional information Cry2 protein binds to ssDNA with high affinity Homo sapiens ?
-
 ?
4.1.99.3 additional information DNA repair protein Synechococcus elongatus PCC 7942 = FACHB-805 ?
-
 ?
4.1.99.3 additional information DNA repair protein Escherichia coli ?
-
 ?
4.1.99.3 thymine
-
 Thermus thermophilus ?
-
 ?
4.1.99.13 T(6-4)T photoproduct (in DNA)
-
 Drosophila melanogaster 2 thymidine residues (in DNA)
-
 ?

Synonyms

EC Number Synonyms Comment Organism
4.1.99.3 CPD-photolyase
-
 Synechococcus elongatus PCC 7942 = FACHB-805
4.1.99.3 CPD-photolyase
-
 Homo sapiens
4.1.99.3 CPD-photolyase
-
 Arabidopsis thaliana
4.1.99.3 CPD-photolyase
-
 Sulfurisphaera tokodaii
4.1.99.3 CPD-photolyase
-
 Thermus thermophilus
4.1.99.3 CPD-photolyase
-
 Escherichia coli
4.1.99.3 CPD-Phr
-
 Sulfurisphaera tokodaii
4.1.99.3 CPD-Phr
-
 Thermus thermophilus
4.1.99.3 CPD-Phr
-
 Escherichia coli
4.1.99.3 Cry-DASH
-
 Arabidopsis thaliana
4.1.99.3 Cry1
-
 Homo sapiens
4.1.99.3 Cry1
-
 Arabidopsis thaliana
4.1.99.3 Cry2
-
 Homo sapiens
4.1.99.3 Cry2
-
 Arabidopsis thaliana
4.1.99.3 cry3
-
 Arabidopsis thaliana
4.1.99.3 cryptochrome-DASH
-
 Arabidopsis thaliana
4.1.99.13 (6-4) photolyase
-
 Drosophila melanogaster
4.1.99.13 (6-4) photolyase
-
 Arabidopsis thaliana
4.1.99.13 (6-4)-Phr
-
 Drosophila melanogaster
4.1.99.13 (6-4)-Phr
-
 Arabidopsis thaliana

Cofactor

EC Number Cofactor Comment Organism Structure
4.1.99.3 5,10-methenyltetrahydrofolate bound at the interface between N-terminal and C-terminal domain Synechococcus elongatus PCC 7942 = FACHB-805
4.1.99.3 5,10-methenyltetrahydrofolate bound at the interface between N-terminal and C-terminal domain Escherichia coli
4.1.99.3 5,10-methenyltetrahydrofolate Cry3 Arabidopsis thaliana
4.1.99.3 8-hydroxy-5-deazariboflavin bound at the interface between N-terminal and C-terminal domain Synechococcus elongatus PCC 7942 = FACHB-805
4.1.99.3 8-hydroxy-5-deazariboflavin bound at the interface between N-terminal and C-terminal domain Escherichia coli
4.1.99.3 8-hydroxy-5-deazariboflavin photolyase can bind next to the natural cofactor 8-hydroxy-5-deazariboflavin also FMN Thermus thermophilus
4.1.99.3 8-iodo-8-demethylriboflavin
-
 Thermus thermophilus
4.1.99.3 FAD a second FAD molecule is present in the antenna pigment binding pocket Sulfurisphaera tokodaii
4.1.99.3 FAD alpha-helical domain is harboring the FAD cofactor, essential for catalysis Synechococcus elongatus PCC 7942 = FACHB-805
4.1.99.3 FAD alpha-helical domain is harboring the FAD cofactor, essential for catalysis Escherichia coli
4.1.99.3 FAD Cry1, which does not bind to DNA, possesses a strongly reduced surface charge around the FAD binding pocket Arabidopsis thaliana
4.1.99.3 FADH2
-
 Synechococcus elongatus PCC 7942 = FACHB-805
4.1.99.3 FMN photolyase can bind next to the natural cofactor 8-hydroxy-5-deazariboflavin also FMN Thermus thermophilus
4.1.99.13 8-hydroxy-5-deazariboflavin
-
 Drosophila melanogaster
4.1.99.13 FAD in the structure of (6-4) photolyase, there is a phosphate anion bound to Glu-243 and Trp-238, close to FAD Arabidopsis thaliana