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IPR007197 is a Radical SAM.
<p>The Radical SAM domain is organised in a fold related to the β-barrel or TIM barrel, in which β-strands are arranged in a barrel-like array, with peripheral helices intervening between β-strands. The [4Fe-4S] clusters and substrates are bound within the barrels, as is typical of TIM barrel enzymes [[cite:PUB00097557], [cite:PUB00097556]].</p> <p>Radical SAM proteins are found in all domains of life and share an unusual Fe-S cluster associated with generation of a free radical by reductive cleavage of SAM and often provide an anaerobic or oxygen-independent mechanism that is found as an aerobic reaction in other proteins. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. These proteins function in DNA precursor, vitamin, cofactor, antibiotic and herbicide biosynthesis and in biodegradation pathways [[cite:PUB00010539], [cite:PUB00015124]].</p> <p>Radical SAM proteins share several common features, notably three strictly conserved cysteine residues generally included in the CxxxCxxC motif. These critical cysteines coordinate the unusual [4Fe-4S]2+/1+ cluster, while SAM serves as ligand for the fourth iron atom and acts as a cofactor or a cosubstrate [[cite:PUB00010539]]. The radical SAM enzymes biochemically characterised to date have in common the cleavage of the [4Fe-4S]1+-SAM complex to [4Fe-4S]2+-Met and the 5'-deoxyadenosyl radical, which abstracts a hydrogen atom from the substrate to initiate a radical mechanism [[cite:PUB00065909], [cite:PUB00097555]].</p>
This description is obtained from EB-eye REST.
GO predictions are based solely on the InterPro-to-GO mappings published by EMBL-EBI, which are in turn based on the mapping of predicted domains to the InterPro dataset. The InterPro-to-GO mapping was last updated on , while the GO metadata was last updated on .
| GO term | Namespace | Name | Definition | Relationships |
|---|---|---|---|---|
| Molecular function | Catalytic activity | Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. | ||
| Molecular function | Iron-sulfur cluster binding | Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms. |
| Transcript | Name | Description | Predicted domains | Domain count |
|---|---|---|---|---|
| – | PREDICTED: oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917-like [Cicer arietinum] gi|502133605|ref|XP_004501826.1| | 14 | ||
| – | PREDICTED: elongator complex protein 3-like [Glycine max] gi|356508774|ref|XP_003523129.1| | 23 | ||
| – | PREDICTED: CDK5RAP1-like protein-like [Glycine max] gi|356540793|ref|XP_003538869.1| | 33 | ||
| – | PREDICTED: probable dual-specificity RNA methyltransferase RlmN-like [Cicer arietinum] gi|502097051|ref|XP_004490899.1| | 22 | ||
| – | PREDICTED: molybdopterin biosynthesis protein CNX2-like [Glycine max] gi|356525689|ref|XP_003531456.1| | 16 | ||
| – | PREDICTED: molybdopterin biosynthesis protein CNX2-like [Glycine max] gi|356525689|ref|XP_003531456.1| | 9 | ||
| – | PREDICTED: lipoyl synthase 2, mitochondrial-like [Glycine max] gi|356543805|ref|XP_003540350.1| | 21 | ||
| – | Biotin synthase [Medicago truncatula] gi|357474135|ref|XP_003607352.1| | 21 | ||
| – | PREDICTED: CDKAL1-like protein-like [Glycine max] gi|356542899|ref|XP_003539902.1| | 29 | ||
| – | PREDICTED: tRNA wybutosine-synthesizing protein 1 homolog isoform X1 [Cicer arietinum] gi|502126020|ref|XP_004499150.1| | 24 | ||
| – | PREDICTED: lipoyl synthase, chloroplastic-like [Glycine max] gi|356575490|ref|XP_003555873.1| | 21 | ||
| – | Dual-specificity RNA methyltransferase RlmN; TAIR: AT2G39670.1 Radical SAM superfamily protein; Swiss-Prot: sp|Q8DG98|RLMN_THEEB Probable dual-specificity RNA methyltransferase RlmN; TrEMBL-Plants: tr|G7KBR0|G7KBR0_MEDTR 23S rRNA m2A2503 methyltransferase; Found in the gene: LotjaGi1g1v0090900 | 24 | ||
| – | Oxygen-independent coproporphyrinogen III oxidase, putative; TAIR: AT5G63290.1 Radical SAM superfamily protein; Swiss-Prot: sp|P73245|Y1917_SYNY3 Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917; TrEMBL-Plants: tr|V7AWC4|V7AWC4_PHAVU Uncharacterized protein; Found in the gene: LotjaGi1g1v0234800 | 14 | ||
| – | Elongator complex protein 3; TAIR: AT5G50320.1 radical SAM domain-containing protein / GCN5-related N-acetyltransferase (GNAT) family protein; Swiss-Prot: sp|Q93ZR1|ELP3_ARATH Elongator complex protein 3; TrEMBL-Plants: tr|A0A151R7U7|A0A151R7U7_CAJCA Elongator complex protein 3; Found in the gene: LotjaGi1g1v0235100 | 24 | ||
| – | TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase; TAIR: AT4G36390.1 Methylthiotransferase; Swiss-Prot: sp|Q8H0V1|CK5P1_ARATH CDK5RAP1-like protein; TrEMBL-Plants: tr|G7KGB3|G7KGB3_MEDTR Radical SAM methylthiotransferase, MiaB/RimO family protein; Found in the gene: LotjaGi2g1v0385400 | 28 | ||
| – | TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase; TAIR: AT4G36390.1 Methylthiotransferase; Swiss-Prot: sp|Q2R1U4|CK5P1_ORYSJ CDK5RAP1-like protein; TrEMBL-Plants: tr|K7LNH5|K7LNH5_SOYBN Uncharacterized protein; Found in the gene: LotjaGi2g1v0385400 | 26 | ||
| – | TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase; TAIR: AT4G36390.1 Methylthiotransferase; Swiss-Prot: sp|Q2R1U4|CK5P1_ORYSJ CDK5RAP1-like protein; TrEMBL-Plants: tr|K7LNH5|K7LNH5_SOYBN Uncharacterized protein; Found in the gene: LotjaGi2g1v0385400 | 26 | ||
| – | TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase; TAIR: AT4G36390.1 Methylthiotransferase; Swiss-Prot: sp|Q2R1U4|CK5P1_ORYSJ CDK5RAP1-like protein; TrEMBL-Plants: tr|K7LNH5|K7LNH5_SOYBN Uncharacterized protein; Found in the gene: LotjaGi2g1v0385400 | 26 | ||
| – | Dual-specificity RNA methyltransferase RlmN; TAIR: AT3G19630.1 Radical SAM superfamily protein; Swiss-Prot: sp|Q6MDD0|RLMN2_PARUW Probable dual-specificity RNA methyltransferase RlmN 2; TrEMBL-Plants: tr|I3T8H2|I3T8H2_LOTJA Uncharacterized protein; Found in the gene: LotjaGi2g1v0459900 | 15 | ||
| – | Dual-specificity RNA methyltransferase RlmN; TAIR: AT3G19630.1 Radical SAM superfamily protein; Swiss-Prot: sp|Q6MDD0|RLMN2_PARUW Probable dual-specificity RNA methyltransferase RlmN 2; TrEMBL-Plants: tr|I3T8H2|I3T8H2_LOTJA Uncharacterized protein; Found in the gene: LotjaGi2g1v0459900 | 7 | ||
| – | GTP 3',8-cyclase; TAIR: AT2G31955.1 cofactor of nitrate reductase and xanthine dehydrogenase 2; Swiss-Prot: sp|Q39055|CNX2_ARATH GTP 3',8-cyclase, mitochondrial; TrEMBL-Plants: tr|I1KTQ5|I1KTQ5_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0127600 | 21 | ||
| – | GTP 3',8-cyclase; TAIR: AT2G31955.3 cofactor of nitrate reductase and xanthine dehydrogenase 2; Swiss-Prot: sp|Q39055|CNX2_ARATH GTP 3',8-cyclase, mitochondrial; TrEMBL-Plants: tr|I1KTQ5|I1KTQ5_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0127600 | 15 | ||
| – | GTP 3',8-cyclase; TAIR: AT2G31955.3 cofactor of nitrate reductase and xanthine dehydrogenase 2; Swiss-Prot: sp|Q39055|CNX2_ARATH GTP 3',8-cyclase, mitochondrial; TrEMBL-Plants: tr|D7MW86|D7MW86_ARALL Putative uncharacterized protein; Found in the gene: LotjaGi3g1v0127600 | 15 | ||
| – | GTP 3',8-cyclase; TAIR: AT2G31955.1 cofactor of nitrate reductase and xanthine dehydrogenase 2; Swiss-Prot: sp|Q39055|CNX2_ARATH GTP 3',8-cyclase, mitochondrial; TrEMBL-Plants: tr|I1KTQ5|I1KTQ5_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0127600 | 21 | ||
| – | GTP 3',8-cyclase; TAIR: AT2G31955.1 cofactor of nitrate reductase and xanthine dehydrogenase 2; Swiss-Prot: sp|Q39055|CNX2_ARATH GTP 3',8-cyclase, mitochondrial; TrEMBL-Plants: tr|I1KTQ5|I1KTQ5_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0127600 | 21 | ||
| – | Lipoyl synthase; TAIR: AT2G20860.1 lipoic acid synthase 1; Swiss-Prot: sp|B7FM45|LIAS_MEDTR Lipoyl synthase, mitochondrial; TrEMBL-Plants: tr|V7BWP4|V7BWP4_PHAVU Lipoyl synthase, mitochondrial; Found in the gene: LotjaGi3g1v0441800 | 21 | ||
| – | Biotin synthase; TAIR: AT2G43360.1 Radical SAM superfamily protein; Swiss-Prot: sp|P54967|BIOB_ARATH Biotin synthase; TrEMBL-Plants: tr|A0A1J7GGN8|A0A1J7GGN8_LUPAN Uncharacterized protein; Found in the gene: LotjaGi3g1v0535800 | 20 | ||
| – | Biotin synthase; TAIR: AT2G43360.1 Radical SAM superfamily protein; Swiss-Prot: sp|P54967|BIOB_ARATH Biotin synthase; TrEMBL-Plants: tr|A0A1J7GGN8|A0A1J7GGN8_LUPAN Uncharacterized protein; Found in the gene: LotjaGi3g1v0535800 | 20 | ||
| – | Biotin synthase; TAIR: AT2G43360.1 Radical SAM superfamily protein; Swiss-Prot: sp|P54967|BIOB_ARATH Biotin synthase; TrEMBL-Plants: tr|A0A1J7GGN8|A0A1J7GGN8_LUPAN Uncharacterized protein; Found in the gene: LotjaGi3g1v0535800 | 20 | ||
| – | TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase; TAIR: AT1G72090.1 Methylthiotransferase; Swiss-Prot: sp|Q6P4Y0|CDKAL_XENTR Threonylcarbamoyladenosine tRNA methylthiotransferase; TrEMBL-Plants: tr|I1LNN6|I1LNN6_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0556600 | 29 | ||
| – | TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase; TAIR: AT1G72090.1 Methylthiotransferase; Swiss-Prot: sp|Q6NS26|CDKAL_XENLA Threonylcarbamoyladenosine tRNA methylthiotransferase; TrEMBL-Plants: tr|I1LNN6|I1LNN6_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0556600 | 29 | ||
| – | Dual-specificity RNA methyltransferase RlmN; TAIR: AT1G60230.1 Radical SAM superfamily protein; Swiss-Prot: sp|A0LQM1|RLMN_SYNFM Dual-specificity RNA methyltransferase RlmN; TrEMBL-Plants: tr|I1KXG4|I1KXG4_SOYBN Uncharacterized protein; Found in the gene: LotjaGi4g1v0165700 | 23 | ||
| – | Dual-specificity RNA methyltransferase RlmN; TAIR: AT1G60230.1 Radical SAM superfamily protein; Swiss-Prot: sp|Q3A2Z4|RLMN_PELCD Dual-specificity RNA methyltransferase RlmN; TrEMBL-Plants: tr|V7C8D7|V7C8D7_PHAVU Uncharacterized protein; Found in the gene: LotjaGi4g1v0165700 | 16 | ||
| – | NADPH--cytochrome P450 reductase; TAIR: AT1G75200.1 flavodoxin family protein / radical SAM domain-containing protein; Swiss-Prot: sp|Q8RXN5|TYW1_ARATH S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase; TrEMBL-Plants: tr|A0A0R0GAG6|A0A0R0GAG6_SOYBN Uncharacterized protein; Found in the gene: LotjaGi5g1v0016300 | 25 | ||
| – | Lipoyl synthase; TAIR: AT5G08415.1 Radical SAM superfamily protein; Swiss-Prot: sp|B9RX57|LISC_RICCO Lipoyl synthase, chloroplastic; TrEMBL-Plants: tr|A0A0R4J646|A0A0R4J646_SOYBN Lipoyl synthase, chloroplastic; Found in the gene: LotjaGi5g1v0345100 | 19 | ||
| – | Lipoyl synthase; TAIR: AT5G08415.1 Radical SAM superfamily protein; Swiss-Prot: sp|B9RX57|LISC_RICCO Lipoyl synthase, chloroplastic; TrEMBL-Plants: tr|A0A0R4J646|A0A0R4J646_SOYBN Lipoyl synthase, chloroplastic; Found in the gene: LotjaGi5g1v0345100 | 21 |
A list of co-occurring predicted domains within the L. japonicus gene space:
| Predicted domain | Source | Observations | Saturation (%) |
|---|---|---|---|
| mobidb-lite | MobiDBLite | 1 | 2.78 |