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Literature summary for 4.1.99.14 extracted from

  • Ghose, S.; Hilmer, J.K.; Bothner, B.; Broderick, J.B.
    Solution phase dynamics of the DNA repair enzyme spore photoproduct lyase as probed by H/D exchange (2014), FEBS Lett., 588, 3023-3029 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
gene splB, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli strain Tuner(DE3)-pLysS Clostridium acetobutylicum

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ [4Fe-4S] cluster Clostridium acetobutylicum

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine Clostridium acetobutylicum in double-helical DNA thymidylyl-(3'->5')-thymidylate
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?
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine Clostridium acetobutylicum ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 in double-helical DNA thymidylyl-(3'->5')-thymidylate
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?

Organism

Organism UniProt Comment Textmining
Clostridium acetobutylicum Q97L63
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Clostridium acetobutylicum ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 Q97L63
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-

Purification (Commentary)

Purification (Comment) Organism
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain Tuner(DE3)-pLysS by nickel affinity chromatography, dialysis under anaerobic conditions, and ultrafiltration Clostridium acetobutylicum

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine in double-helical DNA Clostridium acetobutylicum thymidylyl-(3'->5')-thymidylate
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?
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine in double-helical DNA Clostridium acetobutylicum ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 thymidylyl-(3'->5')-thymidylate
-
?
additional information solution phase dynamics of the DNA repair enzyme spore photoproduct lyase as probed by H/D exchange with HDX as a probe to explore the solution phase conformational dynamics in SPL upon binding to undamaged DNA and dinucleotide 5R-SPTpT and dinucleoside 5R-SP substrates. A 6-mer oligonucleotide, 5'-GCAAGT-3', is used as substrate, which is cleaved to and complement 5'-ACT and TGC-3', overview. Mass spectrometric substrate and product analyses. Enzyme SPL has low affinity for substrate or DNA in the absence of S-adenosyl-L-methionine Clostridium acetobutylicum ?
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?
additional information solution phase dynamics of the DNA repair enzyme spore photoproduct lyase as probed by H/D exchange with HDX as a probe to explore the solution phase conformational dynamics in SPL upon binding to undamaged DNA and dinucleotide 5R-SPTpT and dinucleoside 5R-SP substrates. A 6-mer oligonucleotide, 5'-GCAAGT-3', is used as substrate, which is cleaved to and complement 5'-ACT and TGC-3', overview. Mass spectrometric substrate and product analyses. Enzyme SPL has low affinity for substrate or DNA in the absence of S-adenosyl-L-methionine Clostridium acetobutylicum ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 ?
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?

Synonyms

Synonyms Comment Organism
SPL
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Clostridium acetobutylicum
SplB
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Clostridium acetobutylicum

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
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assay at Clostridium acetobutylicum

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
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assay at Clostridium acetobutylicum

Cofactor

Cofactor Comment Organism Structure
S-adenosyl-L-methionine SAM, SPL is a radical SAM enzyme, enzyme SPL has low affinity for substrate or DNA in the absence of SAM. SAM causes significant structural perturbations regardless of the integrity of the iron-sulfur cluster, consistent with the observation that SAM binds SPL not only via coordination of the iron-sulfur cluster, but also by interactions such as hydrogen bonding, hydrophobic interactions and salt bridges. The amino group of the methionyl moiety of SAM interacts with Ser142 and Asp143 and the carboxylate moiety interacts with Lys174 and Ser195, while the adenine and ribose groups are held in place via hydrogen bonding interactions with Tyr96, Tyr98, Ala234 and Ala273 Clostridium acetobutylicum
[4Fe-4S] cluster
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Clostridium acetobutylicum

General Information

General Information Comment Organism
additional information conformational changes associated with cofactor and substrate binding may serve to provide a solvent inaccessible and protected active site to safely catalyze radical reactions Clostridium acetobutylicum
physiological function on exposure of spores to UV radiation, an unique methylene bridged thymine dimer, 5-thyminyl-5,6-dihydrothymine (spore photoproduct or SP) accumulates as the main photoproduct. This accumulated photo-damage is rapidly repaired upon spore germination. Spore photoproduct lyase (SPL) catalyzes the repair of the UV lesion spore photoproduct (SP) in a reaction dependent on S-adenosyl-L-methionine (SAM) Clostridium acetobutylicum