Radical SAM: Difference between revisions
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* CofH - FO synthase, CofH subunit (cofactor biosynthesis - F420) |
* CofH - FO synthase, CofH subunit (cofactor biosynthesis - F420) |
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* HemN - oxygen-independent coproporphyrinogen III oxidase (cofactor biosynthesis - [[heme]]) |
* HemN - oxygen-independent coproporphyrinogen III oxidase (cofactor biosynthesis - [[heme]]) |
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* NirJ - heme d1 biosynthesis radical SAM protein NirJ (cofactor biosynthesis - heme d1) |
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* LipA - lipoyl synthase (cofactor biosynthesis - lipoyl) |
* LipA - lipoyl synthase (cofactor biosynthesis - lipoyl) |
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* ThiH - thiazole biosynthesis protein ThiH (cofactor biosynthesis - [[thiamine]]) |
* ThiH - thiazole biosynthesis protein ThiH (cofactor biosynthesis - [[thiamine]]) |
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In addition, several non-canonical radical SAM enzymes have been described. These cannot be recognized by the [[Pfam]] [[hidden Markov model]] PF04055, but still use three Cys residues as ligands to a 4Fe4S cluster and produce a radical from S-adenosylmethionine. These include |
In addition, several non-canonical radical SAM enzymes have been described. These cannot be recognized by the [[Pfam]] [[hidden Markov model]] PF04055, but still use three Cys residues as ligands to a 4Fe4S cluster and produce a radical from S-adenosylmethionine. These include |
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* ThiC - thiamine biosynthesis protein ThiC (cofactor biosynthesis - thiamine) |
* ThiC - thiamine biosynthesis protein ThiC (cofactor biosynthesis - thiamine) <ref>{{Cite journal | pmid = 18953358}}</ref> |
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* Dph2 - diphthamide biosynthesis enzyme Dph2 (protein modification - [[diphthamide]] in translation elongation factor 2) (note different radical production, a 3-amino-3-carboxypropyl radical) |
* Dph2 - diphthamide biosynthesis enzyme Dph2 (protein modification - [[diphthamide]] in translation elongation factor 2) (note different radical production, a 3-amino-3-carboxypropyl radical) <ref>{{Cite journal | pmid = 20559380}}</ref> |
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* PhnJ - phosphonate metabolism protein PhnJ (C-P [[phosphonate]] bond cleavage) |
* PhnJ - phosphonate metabolism protein PhnJ (C-P [[phosphonate]] bond cleavage) <ref>{{Cite journal | pmid = 22089136}}</ref> |
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==References== |
==References== |
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Revision as of 19:07, 12 August 2012
Radical SAM is a type of enzymatic reaction in which an iron-sulfur cluster-containing enzyme cleaves S-Adenosyl methionine (SAM) reductively to produce a 5′-deoxyadenosyl 5′-radical as an intermediate.[1] The radical intermediate allows enzymes to perform a wide variety of unusual chemical transformations. Examples of radical SAM enzymes include various enzymes of cofactor biosynthesis, enzyme activation, peptide modification, metalloprotein cluster formation, tRNA modification, lipid metabolism, etc. The vast majority of known radical SAM enzymes belong to the radical SAM superfamily, and have a cysteine-rich motif that matches or resembles CxxxCxxC.
Examples of radical SAM enzymes found within the radical SAM superfamily include:
- BioB - biotin synthase (cofactor biosynthesis - biotin)
- CofG - FO synthase, CofG subunit (cofactor biosynthesis - F420)
- CofH - FO synthase, CofH subunit (cofactor biosynthesis - F420)
- HemN - oxygen-independent coproporphyrinogen III oxidase (cofactor biosynthesis - heme)
- NirJ - heme d1 biosynthesis radical SAM protein NirJ (cofactor biosynthesis - heme d1)
- LipA - lipoyl synthase (cofactor biosynthesis - lipoyl)
- ThiH - thiazole biosynthesis protein ThiH (cofactor biosynthesis - thiamine)
- MoaA - Mo cofactor biosynthesis protein A (cofactor biosynthesis - molybdenum cofactor)
- NifB - cofactor biosynthesis protein nifB (cofactor biosynthesis - FeMo cofactor)
- PqqE - PQQ biosynthesis enzyme (peptide modification / cofactor biosynthesis - PQQ)
- MftC - mycofactocin system maturase (peptide modification/cofactor biosynthesis - predicted)
- AlbA - subtilosin maturase (peptide modification)
- ScfB - SCIFF maturase (peptide modification - predicted)
- PflA - pyruvate formate-lyase activating enzyme (enzyme activation)
- NrdG - anaerobic ribonucleoside-triphosphate reductase activase (enzyme activation)
- AtsB - anaerobic sulfatase activase (enzyme activation)
- PeaB - quinohemoprotein amine dehydrogenase maturation protein (enzyme activation)
- HydE - [FeFe] hydrogenase H-cluster radical SAM maturase (metallocluster assembly)
- HydG - [FeFe] hydrogenase H-cluster radical SAM maturase (metallocluster assembly)
- SplB - spore photoproduct lyase (DNA repair)
- MiaB - tRNA methylthiotransferase (tRNA modification)
- RlmN - 23S rRNA m2A2503 methyltransferase (rRNA modification)
- PylB - pyrrolysine biosynthesis protein PylB (amino acid biosynthesis - pyrrolysine)
- AblA - lysine 2,3-aminomutase (osmolyte biosynthesis - N-epsilon-acetyl-beta-lysine)
- HpnR - hopanoid C-3 methylase (lipid biosynthesis - 3-methylhopanoid production)
- HmdB - 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdB (note unusual CX5CX2C motif)
In addition, several non-canonical radical SAM enzymes have been described. These cannot be recognized by the Pfam hidden Markov model PF04055, but still use three Cys residues as ligands to a 4Fe4S cluster and produce a radical from S-adenosylmethionine. These include
- ThiC - thiamine biosynthesis protein ThiC (cofactor biosynthesis - thiamine) [2]
- Dph2 - diphthamide biosynthesis enzyme Dph2 (protein modification - diphthamide in translation elongation factor 2) (note different radical production, a 3-amino-3-carboxypropyl radical) [3]
- PhnJ - phosphonate metabolism protein PhnJ (C-P phosphonate bond cleavage) [4]
References
- ^ Booker, SJ; Grove, TL (2010). "Mechanistic and functional versatility of radical SAM enzymes". F1000 biology reports. 2: 52. doi:10.3410/B2-52. PMC 2996862. PMID 21152342.
- ^ . PMID 18953358.
{{cite journal}}: Cite journal requires|journal=(help); Missing or empty|title=(help) - ^ . PMID 20559380.
{{cite journal}}: Cite journal requires|journal=(help); Missing or empty|title=(help) - ^ . PMID 22089136.
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