EF-P beta-lysylation protein EpmB is a KamA family radical SAM protein that, together with EpmA, is involved in the beta-lysylation step of the post-translational modification of translation elongation factor P (EF-P) on 'Lys-34'; displays lysine 2,3-aminomutase activity, producing (R)-beta-lysine from (S)-alpha-lysine (L-lysine)
EF-P beta-lysylation protein EpmB; Members of this radical SAM protein subfamily, including ...
15-335
0e+00
EF-P beta-lysylation protein EpmB; Members of this radical SAM protein subfamily, including yjeK in E. coli, form a distinctive clade, homologous to lysine-2,3-aminomutase of Bacillus, Clostridium, and methanogenic archaea. Members of this family are found in E. coli, Buchnera, Yersinia, etc. The gene symbol is now reassigned as EpmB (Elongation factor P Modification B). [Protein fate, Protein modification and repair]
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Pssm-ID: 163533 Cd Length: 321 Bit Score: 573.88 E-value: 0e+00
EF-P beta-lysylation protein EpmB; Members of this radical SAM protein subfamily, including ...
15-335
0e+00
EF-P beta-lysylation protein EpmB; Members of this radical SAM protein subfamily, including yjeK in E. coli, form a distinctive clade, homologous to lysine-2,3-aminomutase of Bacillus, Clostridium, and methanogenic archaea. Members of this family are found in E. coli, Buchnera, Yersinia, etc. The gene symbol is now reassigned as EpmB (Elongation factor P Modification B). [Protein fate, Protein modification and repair]
Pssm-ID: 163533 Cd Length: 321 Bit Score: 573.88 E-value: 0e+00
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
114-236
6.06e-07
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.
Pssm-ID: 100105 [Multi-domain] Cd Length: 204 Bit Score: 49.25 E-value: 6.06e-07
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
119-263
1.20e-06
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: 47.91 E-value: 1.20e-06
EF-P beta-lysylation protein EpmB; Members of this radical SAM protein subfamily, including ...
15-335
0e+00
EF-P beta-lysylation protein EpmB; Members of this radical SAM protein subfamily, including yjeK in E. coli, form a distinctive clade, homologous to lysine-2,3-aminomutase of Bacillus, Clostridium, and methanogenic archaea. Members of this family are found in E. coli, Buchnera, Yersinia, etc. The gene symbol is now reassigned as EpmB (Elongation factor P Modification B). [Protein fate, Protein modification and repair]
Pssm-ID: 163533 Cd Length: 321 Bit Score: 573.88 E-value: 0e+00
KamA family protein; This model represents essentially the whole of E. coli YjeK and of some ...
2-328
9.70e-161
KamA family protein; This model represents essentially the whole of E. coli YjeK and of some of its apparent orthologs. YodO in Bacillus subtilis, a family member which is longer protein by an additional 100 residues, is characterized as a lysine 2,3-aminomutase with iron, sulphide and pyridoxal 5'-phosphate groups. The homolog MJ0634 from M. jannaschii is preceded by nearly 200 C-terminal residues. This family shows similarity to molybdenum cofactor biosynthesis protein MoaA and related proteins. Note that the E. coli homolog was expressed in E. coli and purified and found not to display display lysine 2,3-aminomutase activity. Active site residues are found in 100 residue extension in B. subtilis. Name changed to KamA family protein. [Cellular processes, Adaptations to atypical conditions]
Pssm-ID: 272980 Cd Length: 331 Bit Score: 452.37 E-value: 9.70e-161
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
114-236
6.06e-07
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.
Pssm-ID: 100105 [Multi-domain] Cd Length: 204 Bit Score: 49.25 E-value: 6.06e-07
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
120-231
9.75e-07
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: 47.98 E-value: 9.75e-07
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
119-263
1.20e-06
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: 47.91 E-value: 1.20e-06
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
119-172
2.44e-04
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG, which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]
Pssm-ID: 274164 [Multi-domain] Cd Length: 192 Bit Score: 41.58 E-value: 2.44e-04
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
111-169
1.18e-03
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.
Pssm-ID: 433138 [Multi-domain] Cd Length: 137 Bit Score: 38.69 E-value: 1.18e-03
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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Functional characterization of the conserved domain architecture found on the query.
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