radical SAM family protein may generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity; contains a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; transfers a single electron from the iron-sulfur cluster to SAM leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
9-223
3.73e-144
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
The actual alignment was detected with superfamily member TIGR04322:
Pssm-ID: 450244 Cd Length: 215 Bit Score: 400.89 E-value: 3.73e-144
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Members of this radical ...
9-223
3.73e-144
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Members of this radical SAM domain protein family appear to be the E. coli form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in species that lack known forms of QueE but usually are not found in queuosine biosynthesis operons. Members of this family tend to form bi-directional best hit matches to members of known (TIGR03365) and putative (TIGR03963) QueE families from other lineages.
Pssm-ID: 275126 Cd Length: 215 Bit Score: 400.89 E-value: 3.73e-144
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
2-222
5.35e-80
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic radical activating enzyme NrdG/QueE is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440367 [Multi-domain] Cd Length: 205 Bit Score: 238.11 E-value: 5.35e-80
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Members of this radical ...
9-223
3.73e-144
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Members of this radical SAM domain protein family appear to be the E. coli form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in species that lack known forms of QueE but usually are not found in queuosine biosynthesis operons. Members of this family tend to form bi-directional best hit matches to members of known (TIGR03365) and putative (TIGR03963) QueE families from other lineages.
Pssm-ID: 275126 Cd Length: 215 Bit Score: 400.89 E-value: 3.73e-144
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
2-222
5.35e-80
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic radical activating enzyme NrdG/QueE is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440367 [Multi-domain] Cd Length: 205 Bit Score: 238.11 E-value: 5.35e-80
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; ...
5-125
8.51e-22
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Members of this radical SAM domain protein family appear to be a form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in preQ0 operons species that lack members of related protein family TIGR03365.
Pssm-ID: 275145 [Multi-domain] Cd Length: 210 Bit Score: 88.82 E-value: 8.51e-22
7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; This uncharacterized enzyme, ...
4-160
1.07e-19
7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; This uncharacterized enzyme, designated QueE, participates in the biosynthesis, from GTP, of 7-cyano-7-deazaguanosine, also called preQ0 because in many species it is a precursor of queuosine. In most Archaea, it is instead the precursor of a different tRNA modified base, archaeosine. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 274545 Cd Length: 238 Bit Score: 83.95 E-value: 1.07e-19
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Members of ...
3-126
4.21e-18
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Members of this radical SAM domain protein family appear to be the Clostridial form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in preQ0 operons species that lack members of related protein family TIGR03365. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 188478 [Multi-domain] Cd Length: 219 Bit Score: 79.35 E-value: 4.21e-18
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
71-122
2.43e-04
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism];
Pssm-ID: 440301 [Multi-domain] Cd Length: 159 Bit Score: 40.27 E-value: 2.43e-04
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
30-123
3.58e-04
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Pssm-ID: 427681 [Multi-domain] Cd Length: 159 Bit Score: 39.82 E-value: 3.58e-04
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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