Literature summary for 4.1.99.13 extracted from

Zhang, F.; Scheerer, P.; Oberpichler, I.; Lamparter, T.; Krauss, N.
Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore (2013), Proc. Natl. Acad. Sci. USA, 110, 7217-7222.

Search for more literature for 4.1.99.13

Cloned(Commentary)

Cloned (Comment)	Organism
recombinant expression of His-tagged enzyme in Escherichia coli	Agrobacterium tumefaciens

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant His-tagged enzyme, hanging drop vapor diffusion method, mixing of 0.005 ml of protein in 12.5 mM Tris (hydroxymethyl) amino methane, 1.25 mM EDTA, 2.5% v/v glycerol, 75 mM sodium chloride, pH 7.8, with 0.005 ml of reservoir solution containing 2-6% w/v PEG400, 100 mM 2-(N-morpholino) ethanesulfonic acid buffer, pH 6.0, 25°C, 3-7 days, X-ray diffraction structure determination and analysis at 1.45-1.95 A resolution	Agrobacterium tumefaciens

Crystallization (Comment)

Organism

purified recombinant His-tagged enzyme, hanging drop vapor diffusion method, mixing of 0.005 ml of protein in 12.5 mM Tris (hydroxymethyl) amino methane, 1.25 mM EDTA, 2.5% v/v glycerol, 75 mM sodium chloride, pH 7.8, with 0.005 ml of reservoir solution containing 2-6% w/v PEG400, 100 mM 2-(N-morpholino) ethanesulfonic acid buffer, pH 6.0, 25°C, 3-7 days, X-ray diffraction structure determination and analysis at 1.45-1.95 A resolution

Agrobacterium tumefaciens

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Fe2+	the prokaryotic enzyme contains a a [4Fe-4S] cluster bound to the catalytic domain	Agrobacterium tumefaciens

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
(6-4) photoproduct (in DNA)	Agrobacterium tumefaciens	PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts	2 pyrimidine residues (in DNA)	-	?
(6-4) photoproduct (in DNA)	Agrobacterium tumefaciens C58 / ATCC 33970	PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts	2 pyrimidine residues (in DNA)	-	?

Organism

Organism	UniProt	Comment	Textmining
Agrobacterium tumefaciens	A9CH39	gene phrB	-
Agrobacterium tumefaciens C58 / ATCC 33970	A9CH39	gene phrB	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography and gel filtration under dim light conditions or in darkness	Agrobacterium tumefaciens

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
(6-4) photoproduct (in DNA)	PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts	Agrobacterium tumefaciens	2 pyrimidine residues (in DNA)	-	?
(6-4) photoproduct (in DNA)	substrates are single stranded or double stranded DNA probe comprising the AGGT(6-4)TGGC or GCGGT(6-4)TGGCG paired with TCGCCAACCGCT. PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts, substrate binding structure, detailed overview. Arg183 is part of the loop region connecting alpha7 and alpha8	Agrobacterium tumefaciens	2 pyrimidine residues (in DNA)	-	?
(6-4) photoproduct (in DNA)	PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts	Agrobacterium tumefaciens C58 / ATCC 33970	2 pyrimidine residues (in DNA)	-	?
(6-4) photoproduct (in DNA)	substrates are single stranded or double stranded DNA probe comprising the AGGT(6-4)TGGC or GCGGT(6-4)TGGCG paired with TCGCCAACCGCT. PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts, substrate binding structure, detailed overview. Arg183 is part of the loop region connecting alpha7 and alpha8	Agrobacterium tumefaciens C58 / ATCC 33970	2 pyrimidine residues (in DNA)	-	?

Synonyms

Synonyms	Comment	Organism
(6-4) photolyase	-	Agrobacterium tumefaciens
PhrB	-	Agrobacterium tumefaciens

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Agrobacterium tumefaciens

Cofactor

Cofactor	Comment	Organism	Structure
6,7-dimethyl-8-ribityllumazine	the PhrB structure contains 6,7-dimethyl-8-ribityllumazine as an antenna chromophore, binding site-structure, overview	Agrobacterium tumefaciens
FAD	chromophore, assumes a prototypical U-shaped conformation	Agrobacterium tumefaciens

General Information

General Information	Comment	Organism
evolution	(6-4)photolyases are broadly distributed in prokaryotes. the PhrB-like photolyases branched at the base of the evolution of the cryptochrome/photolyase family. The prokaryotic (6-4) photolyases are the ancestors of the cryptochrome/photolyase family	Agrobacterium tumefaciens
additional information	the His365-His366-X-X-Arg369 motif is located within the proposed DNA lesion contact site of PhrB. This motif is structurally conserved in eukaryotic (6-4) photolyases for which the second His is essential for the (6-4) photolyase function. His366 in PhrB is stabilized by van der Waals contacts with Leu370 and Met410. The enzyme has a C-terminal extension	Agrobacterium tumefaciens