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Literature summary for 4.1.99.14 extracted from

  • Yang, L.; Adhikari, J.; Gross, M.L.; Li, L.
    Kinetic isotope effects and hydrogen/deuterium exchange reveal large conformational changes during the catalysis of the Clostridium acetobutylicum spore photoproduct lyase (2017), Photochem. Photobiol., 93, 331-342 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 4.1.99.14

Cloned(Commentary)

Cloned (Comment) Organism
gene splB, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) from plasmid pDB 1282 that confers ampicillin resistance and harbors an Escherichia coli operon that is involved in the biosynthesis of FeS clusters, it may facilitate incorporation of the FeS clusters into the apoprotein of SPL 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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Reaction

Reaction Comment Organism Reaction ID
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA) spore photoproduct lyase (SPL) repairs 5-thyminyl-5,6-dihydrothymine (i.e., the spore photoproduct (SP)) using a radical transfer pathway that includes at least a cysteine and a tyrosine in germinating endospores. The cysteine (at position 74) and tyrosine are located on the opposite sides of a substrate binding pocket that has to collapse to bring the two residues into proximity, enabling the C->Y radical passage Clostridium acetobutylicum
a

Source Tissue

Source Tissue Comment Organism Textmining

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
-
 ?
(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
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 ?
additional information substrate and product analysis by mass spectrometry Clostridium acetobutylicum ?
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 ?
additional information substrate and product analysis by mass spectrometry 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
SPL(Ca)
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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
22
-
 assay at room temperature Clostridium acetobutylicum

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7
-
 assay at Clostridium acetobutylicum

Cofactor

Cofactor Comment Organism Structure
S-adenosyl-L-methionine SPL is a radical SAM enzyme Clostridium acetobutylicum
[4Fe-4S] cluster SPL is an iron-sulfur enzyme. Once reduced to the 1+ oxidation state, the cluster can then donate an electron to the sulfonium ion of SAM to cleave it reductively to produce a 5'-deoxyadenosyl radical and a methionine. The 5'-deoxyadenosyl radical abstracts the H6proR atom to initiate the SP repair process, and the resulting thymine allylic radical receives an H-atom from a conserved cysteine Clostridium acetobutylicum

General Information

General Information Comment Organism
evolution enzyme SPL belongs to the radical SAM (S-adenosylmethionine) enzyme superfamily. The superfamily is defined by the characteristic tri-cysteinyl motif: CX3CX2C that binds to a [4Fe-4S] cluster Clostridium acetobutylicum
additional information the repair of dinucleotide SP TpT by SPL(Ca) is 8-10-fold slower than that by SPL from Bacillus subtilis. The process also generates a large portion of the aborted product TpTSO2-. SPL(Ca) exhibits apparent (DV) kinetic isotope effects (KIEs) of about 6 and abnormally large competitive (DV/K) KIEs (about 20), both of which are much larger than the KIEs observed in from Bacillus subtilis. Clostridium acetobutilicum SPL(Ca) possesses a flexible active site and readily undergoes conformational changes during catalysis. Apparent (DV) kinetics isotope effect (KIE) determination, competitive (DV/K) KIE determination, and HDX-MS analysis of enzyme reaction and structure, overview Clostridium acetobutylicum
physiological function spore photoproduct lyase (SPL) catalyzes the direct reversal of a thymine dimer 5-thyminyl-5,6 dihydrothymine, i.e., the spore photoproduct (SP) to two thymine residues in germinating endospores Clostridium acetobutylicum