4.1.99.14: spore photoproduct lyase
This is an abbreviated version!
For detailed information about spore photoproduct lyase, go to the full flat file.
Word Map on EC 4.1.99.14
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4.1.99.14
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photoproducts
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thymine
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5-thyminyl-5,6-dihydrothymine
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s-adenosylmethionine
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endospores
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uv-irradiated
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5\'-deoxyadenosyl
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thymine-thymine
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spla
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5'-deoxyadenosine
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h-atoms
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beta-scission
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photolyases
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sp-containing
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cxxxcxxc
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deoxyadenosyl
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thiyl
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photolesion
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forespore
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radical-based
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spore-specific
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analysis
- 4.1.99.14
- photoproducts
- thymine
- 5-thyminyl-5,6-dihydrothymine
- s-adenosylmethionine
- endospores
-
uv-irradiated
-
5\'-deoxyadenosyl
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thymine-thymine
- spla
- 5'-deoxyadenosine
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h-atoms
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beta-scission
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photolyases
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sp-containing
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cxxxcxxc
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deoxyadenosyl
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thiyl
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photolesion
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forespore
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radical-based
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spore-specific
- analysis
Reaction
Synonyms
Bs SP lyase, Bs SPL, Ca SP lyase, Gt SP lyase, Gt SPL, GTNG_2348, More, SP lyase, SPL, SPL(Ca), spl-1, SplB, SplG, spore photoproduct lyase
ECTree
Advanced search results
Reaction
Reaction on EC 4.1.99.14 - spore photoproduct lyase
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(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
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(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
reaction mechanism, overview
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(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
reaction mechanism, two different routes, overview
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(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
the enzyme catalyzes the spore photoproduct repair reaction and combines specific features of radical S-adenosyl-L-methionine and DNA repair enzymes to enable a complex radical-based repair reaction to take place
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
the enzyme catalyzes the spore photoproduct repair reaction via a radical mediated direct reverse mechanism. At the 1+ oxidation state, the [4Fe-4S] cluster provides an electron to the S-adenosyl-L-methionine, which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the C-S bond associated with the sulfonium ion in S-adenosyl-L-methionine, generating a reactive 5'-deoxyadenosyl radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of spore photoproduct to initiate the repair process. The resulting spore photoproduct radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired thymidylyl-(3'->5')-thymidylate. Cys141 is involved in the catalytic mechanism as the potential H atom donor to the thymine methyl radical, reaction mechanism, detailed overview. A a thiyl radical is subsequently generated on Cys141
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(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
the enzyme is a radical S-adenosyl-L-methionine enzyme, which uses a [4Fe-4S]1+ cluster to reduce the S-adenosyl-L-methionine, generating a catalytic 5'-deoxyadenosyl radical. This in turn abstracts an H atom from spore product, generating an spore product radical that undergoes beta scission to form a repaired 5'-thymine and a 3'-thymine allylic radical. A conserved cysteine donates an H atom to the thymine radical, resulting in a putative thiyl radical. Two conserved tyrosines are also critical in enzyme catalysis. One, Y99, is downstream of the cysteine, suggesting that the enzyme uses a hydrogen atom transfer pathway with a pair of cysteine-tyrosine residues to regenerate S-adenosyl-L-methionine. The other tyrosine, Y97, has a structural role to facilitate S-adenosyl-L-methionine binding. It may also contribute to the S-adenosyl-L-methionine regeneration process by interacting with the putative Y99 radical and/or 5-dA radical intermediates to lower the energy barrier for the second H-abstraction step. Irreversible first step and tightly coupled radical relay mechanism
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(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SP repair is initiated by abstraction of a H atom from C6 of SP. The SP(C6) substrate radical is thought to promote a radical-mediated beta-scission of the C-C bond linking the two thymines; the resulting product radical then abstracts an H atom to generate repaired thymine. S-adenosyl-L-methionine as a substrate utilize a defined dinucleotide or dinucleoside SP, rather than SP in intact DNA, suggesting the possibility that stoichiometric SAM cleavage is favored with non-optimal substrates
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SPL is a radical S-adenosylmethionine (SAM) enzyme, reaction mechanism, detailed overview. Radicals are quenched to close the catalytic cycle. The characteristic CXXXCXXC motif is involved in catalysis, although other tri-cysteine motifs may also facilitate this radical chemistry. Enzyme SPL directly directly reverts SP thymine photodimer. The conserved solvent-accessible cysteine 140 is the intrinsic hydrogen atom donor
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SPL is a radical S-adenosylmethionine (SAM) enzyme, reaction mechanism, detailed overview. Radicals are quenched to close the catalytic cycle. The characteristic CXXXCXXC motif is involved in catalysis, although other tri-cysteine motifs may also facilitate this radical chemistry. Enzyme SPL directly reverts SP thymine photodimer. The conserved solvent-accessible cysteine 141 is the intrinsic hydrogen atom donor to the thymine radical
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SPL is a radical S-adenosylmethionine (SAM) enzyme, via a 3'-thymine allylic radical intermediate, reaction mechanism, detailed overview
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SPL is a radical S-adenosylmethionine (SAM) enzyme, via a 3'-thymine allylic radical intermediate, reaction mechanism, detailed overview
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SPL is a radical S-adenosylmethionine (SAM) enzyme, via a 3'-thymine allylic radical intermediate, reaction mechanism, detailed overview
(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
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
thymine dimers can be repaired via direct reversal mechanism
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
reaction mechanism, overview
-
-
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
the enzyme is a radical S-adenosyl-L-methionine enzyme, which uses a [4Fe-4S]1+ cluster to reduce the S-adenosyl-L-methionine, generating a catalytic 5'-deoxyadenosyl radical. This in turn abstracts an H atom from spore product, generating an spore product radical that undergoes beta scission to form a repaired 5'-thymine and a 3'-thymine allylic radical. A conserved cysteine donates an H atom to the thymine radical, resulting in a putative thiyl radical. Two conserved tyrosines are also critical in enzyme catalysis. One, Y99, is downstream of the cysteine, suggesting that the enzyme uses a hydrogen atom transfer pathway with a pair of cysteine-tyrosine residues to regenerate S-adenosyl-L-methionine. The other tyrosine, Y97, has a structural role to facilitate S-adenosyl-L-methionine binding. It may also contribute to the S-adenosyl-L-methionine regeneration process by interacting with the putative Y99 radical and/or 5-dA radical intermediates to lower the energy barrier for the second H-abstraction step. Irreversible first step and tightly coupled radical relay mechanism
-
-
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
the enzyme catalyzes the spore photoproduct repair reaction via a radical mediated direct reverse mechanism. At the 1+ oxidation state, the [4Fe-4S] cluster provides an electron to the S-adenosyl-L-methionine, which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the C-S bond associated with the sulfonium ion in S-adenosyl-L-methionine, generating a reactive 5'-deoxyadenosyl radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of spore photoproduct to initiate the repair process. The resulting spore photoproduct radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired thymidylyl-(3'->5')-thymidylate. Cys141 is involved in the catalytic mechanism as the potential H atom donor to the thymine methyl radical, reaction mechanism, detailed overview. A a thiyl radical is subsequently generated on Cys141
-
-
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
thymine dimers can be repaired via direct reversal mechanism
-
-
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SPL is a radical S-adenosylmethionine (SAM) enzyme, reaction mechanism, detailed overview. Radicals are quenched to close the catalytic cycle. The characteristic CXXXCXXC motif is involved in catalysis, although other tri-cysteine motifs may also facilitate this radical chemistry. Enzyme SPL directly reverts SP thymine photodimer. The conserved solvent-accessible cysteine 141 is the intrinsic hydrogen atom donor to the thymine radical
-
-
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SPL is a radical S-adenosylmethionine (SAM) enzyme, via a 3'-thymine allylic radical intermediate, reaction mechanism, detailed overview
-
-
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SP repair is initiated by abstraction of a H atom from C6 of SP. The SP(C6) substrate radical is thought to promote a radical-mediated beta-scission of the C-C bond linking the two thymines; the resulting product radical then abstracts an H atom to generate repaired thymine. S-adenosyl-L-methionine as a substrate utilize a defined dinucleotide or dinucleoside SP, rather than SP in intact DNA, suggesting the possibility that stoichiometric SAM cleavage is favored with non-optimal substrates
Clostridium acetobutylicum ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
-
-
(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 ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
-
-
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SPL is a radical S-adenosylmethionine (SAM) enzyme, via a 3'-thymine allylic radical intermediate, reaction mechanism, detailed overview
Clostridium acetobutylicum ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
-
-
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SPL is a radical S-adenosylmethionine (SAM) enzyme, reaction mechanism, detailed overview. Radicals are quenched to close the catalytic cycle. The characteristic CXXXCXXC motif is involved in catalysis, although other tri-cysteine motifs may also facilitate this radical chemistry. Enzyme SPL directly directly reverts SP thymine photodimer. The conserved solvent-accessible cysteine 140 is the intrinsic hydrogen atom donor
-
-
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
SPL is a radical S-adenosylmethionine (SAM) enzyme, via a 3'-thymine allylic radical intermediate, reaction mechanism, detailed overview
-
-
(5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'->5')-thymidylate (in double-helical DNA)
the enzyme catalyzes the spore photoproduct repair reaction and combines specific features of radical S-adenosyl-L-methionine and DNA repair enzymes to enable a complex radical-based repair reaction to take place
-
-