Literature summary for 4.1.99.13 extracted from

Holub, D.; Ma, H.; Krauss, N.; Lamparter, T.; Elstner, M.; Gillet, N.
Functional role of an unusual tyrosine residue in the electron transfer chain of a prokaryotic (6-4) photolyase (2018), Chem. Sci., 9, 1259-1272 .

Search for more literature for 4.1.99.13

Cloned(Commentary)

Cloned (Comment)	Organism
gene phrB, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain ER2566	Agrobacterium fabrum

Protein Variants

Protein Variants	Comment	Organism
Y391A	site-directed mutagenesis, Tyr391 replacement by alanine blocks photoreduction	Agrobacterium fabrum
Y391F	site-directed mutagenesis, Tyr391 replacement by phenylalanine does not block photoreduction	Agrobacterium fabrum
Y391W	site-directed mutagenesis, replacement of Tyr391 by Trp results in loss of FAD and DMRL chromophores, Trp might participate in the electron transfer cascade	Agrobacterium fabrum

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
(6-4) photoproduct (in DNA)	Agrobacterium fabrum	-	2 pyrimidine residues (in DNA)	-	?
(6-4) photoproduct (in DNA)	Agrobacterium fabrum C58 / ATCC 33970	-	2 pyrimidine residues (in DNA)	-	?

Organism

Organism	UniProt	Comment	Textmining
Agrobacterium fabrum	A9CH39	-	-
Agrobacterium fabrum C58 / ATCC 33970	A9CH39	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain ER2566 by nickel affinity chromatography and gel filtration	Agrobacterium fabrum

Reaction

Reaction	Comment	Organism	Reaction ID
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)	photoreduction of PhrB differs from the typical pattern because the amino acid of the electron cascade next to FAD is a tyrosine (Tyr391), whereas photolyases and cryptochromes of other groups have a tryptophan as direct electron donor of FAD. Residues Trp342 and Trp390 are essential for charge transfer, Trp342 is located at the periphery of PhrB, while Trp390 connects Trp342 and Tyr391. Charge transfer occurs via the triad 391-390-342. Charge transfer simulations reveal an unusual stabilization of the positive charge on site 391 compared to other photolyases or cryptochromes. Water molecules near Tyr391 offer a polar environment which stabilizes the positive charge on this site, thereby lowering the energetic barrier intrinsic to tyrosine. This opens a second charge transfer channel in addition to tunnelling through the tyrosine barrier, based on hopping and therefore transient oxidation of Tyr391, which enables a fast charge transfer similar to proteins utilizing a tryptophan-triad	Agrobacterium fabrum	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
(6-4) photoproduct (in DNA)	-	Agrobacterium fabrum	2 pyrimidine residues (in DNA)	-	?
(6-4) photoproduct (in DNA)	-	Agrobacterium fabrum C58 / ATCC 33970	2 pyrimidine residues (in DNA)	-	?

Synonyms

Synonyms	Comment	Organism
bacterial (6-4) photolyase	-	Agrobacterium fabrum
PhrB	-	Agrobacterium fabrum
prokaryotic (6-4) photolyase	-	Agrobacterium fabrum

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
25	-	assay at	Agrobacterium fabrum

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7	-	assay at	Agrobacterium fabrum

Cofactor

Cofactor	Comment	Organism	Structure
FAD	-	Agrobacterium fabrum

General Information

General Information	Comment	Organism
evolution	the bacterial (6-4) photolyase PhrB belongs to a phylogenetically ancient group. Photoreduction of PhrB differs from the typical pattern because the amino acid of the electron cascade next to FAD is a tyrosine (Tyr391), whereas photolyases and cryptochromes of other groups have a tryptophan as direct electron donor of FAD. Evolution of the first site of the redox chain has just been possible by tuning the protein structure and environment to manage a downhill hole transfer process from FAD to solvent	Agrobacterium fabrum
malfunction	replacement of Tyr391 by phenylalanine does not block photoreduction, while replacement by alanine blocks photoreduction, replacement of Tyr391 by Trp results in loss of FAD and DMRL chromophores	Agrobacterium fabrum
additional information	tunnelling matrix calculations show that tyrosine or phenylalanine can be involved in a productive bridged electron transfer between FAD and Trp390, in line with experimental findings, structure modeling of wild-type and mutant enzymes. Unusual stabilization of the positive charge on site 391 compared to other photolyases or cryptochromes. Mutational analyses of oligonucleotide sequences for DNA repair studies. Charge migration pathway from the protein surface Trp342 to FAD via Trp390 and Tyr391, light induced consecutive electron transfers, structures. Model structures and molecular dynamics simulations, overview	Agrobacterium fabrum

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Release 2023.1 (January 2023)