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Literature summary for 4.1.99.14 extracted from
- DNA repair by the radical SAM enzyme spore photoproduct lyase from biochemistry to structural investigations (2017), Photochem. Photobiol., 93, 67-77 .
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| C140A | site-directed mutagenesis, mutant enzyme activity analysis using an SP dinucleoside and an SP-containing oligonucleotide | Geobacillus thermodenitrificans |
| C140A/S76C | site-directed mutagenesis, contrary to the C140A mutant, the double mutant repaires the DNA lesion without generating DNA adducts. Furthermore, in the crystal structure, the mutant S76C is shown to be at 4.1 A from the methylene bridge of SP which is a shorter distance than the one reported for the wild-type enzyme | Geobacillus thermodenitrificans |
| C140S | site-directed mutagenesis, mutant enzyme activity analysis using an SP dinucleoside and an SP-containing oligonucleotide | Geobacillus thermodenitrificans |
| C141A | site-directed mutagenesis, mutant enzyme activity analysis using an SP dinucleoside and an SP-containing oligonucleotide | Bacillus subtilis |
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 | Geobacillus thermodenitrificans | in double-helical DNA | thymidylyl-(3'->5')-thymidylate | - |
? |  |
| (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine | Clostridium acetobutylicum | in double-helical DNA | thymidylyl-(3'->5')-thymidylate | - |
? | |
| (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine | Bacillus subtilis | in double-helical DNA | thymidylyl-(3'->5')-thymidylate | - |
? | |
| (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine | Bacillus subtilis 168 | in double-helical DNA | thymidylyl-(3'->5')-thymidylate | - |
? | |
| (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 | - |
? | |
| (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine | Geobacillus thermodenitrificans NG80-2 | in double-helical DNA | thymidylyl-(3'->5')-thymidylate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bacillus subtilis | P37956 | - |
- |
| Bacillus subtilis 168 | P37956 | - |
- |
| Clostridium acetobutylicum | Q97L63 | - |
- |
| Clostridium acetobutylicum ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 | Q97L63 | - |
- |
| Geobacillus thermodenitrificans | A4IQU1 | - |
- |
| Geobacillus thermodenitrificans NG80-2 | A4IQU1 | - |
- |
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) | SPL is a radical S-adenosylmethionine (SAM) enzyme, via a 3'-thymine allylic radical intermediate, reaction mechanism, detailed overview | Geobacillus thermodenitrificans | |
| (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 | |
| (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 | Bacillus subtilis |
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 | Geobacillus thermodenitrificans | thymidylyl-(3'->5')-thymidylate | - |
? | |
| (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 | Bacillus subtilis | thymidylyl-(3'->5')-thymidylate | - |
? | |
| (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine | in double-helical DNA | Bacillus subtilis 168 | 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 | - |
? | |
| (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine | in double-helical DNA | Geobacillus thermodenitrificans NG80-2 | thymidylyl-(3'->5')-thymidylate | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| Bs SP lyase | - |
Bacillus subtilis |
| Ca SP lyase | - |
Clostridium acetobutylicum |
| Gt SP lyase | - |
Geobacillus thermodenitrificans |
| SP lyase | - |
Geobacillus thermodenitrificans |
| SP lyase | - |
Clostridium acetobutylicum |
| SP lyase | - |
Bacillus subtilis |
| SPL | - |
Geobacillus thermodenitrificans |
| SPL | - |
Clostridium acetobutylicum |
| SPL | - |
Bacillus subtilis |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| S-adenosyl-L-methionine | SPL is a radical SAM enzyme | Geobacillus thermodenitrificans | |
| S-adenosyl-L-methionine | SPL is a radical SAM enzyme | Clostridium acetobutylicum | |
| S-adenosyl-L-methionine | SPL is a radical SAM enzyme | Bacillus subtilis | |
| [4Fe-4S] cluster | SPL is an iron-sulfur enzyme | Geobacillus thermodenitrificans | |
| [4Fe-4S] cluster | SPL is an iron-sulfur enzyme | Clostridium acetobutylicum | |
| [4Fe-4S] cluster | SPL is an iron-sulfur enzyme | Bacillus subtilis | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the enzyme is a member of the radical SAM superfamily, but SP lyase is the only known radical SAM enzyme to date catalyzing DNA repair. Clostridia SP lyases possess a conserved cysteine residue upstream the radical SAM motif (Cys74), which is substituted by a serine residue in Bacilli SP lyases | Bacillus subtilis |
| evolution | the enzyme is a member of the radical SAM superfamily, but SP lyase is the only known radical SAM enzyme to date catalyzing DNA repair. Clostridia SP lyases possess a conserved cysteine residue upstream the radical SAM motif (Cys74), which is substituted by a serine residue in Bacilli SP lyases. Cys74 in Ca SP lyase occupies a critical location similar to Cys140 in Gt SP lyase | Clostridium acetobutylicum |
| evolution | the enzyme is a member of the radical SAM superfamily, but SP lyase is the only known radical SAM enzyme to date catalyzing DNA repair. Cys74 in Ca SP lyase occupies a critical location similar to Cys140 in Gt SP lyase | Geobacillus thermodenitrificans |
| malfunction | contrary to the C140A mutant, the double mutant repaires the DNA lesion without generating DNA adducts. Furthermore, in the crystal structure, the mutant S76C is shown to be at 4.1 A from the methylene bridge of SP which is a shorter distance than the one reported for the wild-type enzyme | Geobacillus thermodenitrificans |
| additional information | the catalytic the cysteine residue is localized in a loop within the active site and in a very close proximity to the substrate at a distance of 4.5 A from the methylene bridge of the SP dimer | Geobacillus thermodenitrificans |
| additional information | the catalytic the cysteine residue is localized in a loop within the active site and in a very close proximity to the substrate at a distance of 4.5 A from the methylene bridge of the SP dimer | Bacillus subtilis |
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