oxygen-independent coproporphyrinogen III oxidase; This model represents HemN, the ...
6-457
0e+00
oxygen-independent coproporphyrinogen III oxidase; This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]
The actual alignment was detected with superfamily member TIGR00538:
Pssm-ID: 129629 [Multi-domain] Cd Length: 455 Bit Score: 772.81 E-value: 0e+00
oxygen-independent coproporphyrinogen III oxidase; This model represents HemN, the ...
6-457
0e+00
oxygen-independent coproporphyrinogen III oxidase; This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]
Pssm-ID: 129629 [Multi-domain] Cd Length: 455 Bit Score: 772.81 E-value: 0e+00
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase ...
24-445
0e+00
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase [Coenzyme transport and metabolism]; Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase is part of the Pathway/BioSystem: Heme biosynthesis
Pssm-ID: 440400 [Multi-domain] Cd Length: 400 Bit Score: 512.03 E-value: 0e+00
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
52-270
7.39e-56
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Pssm-ID: 214792 [Multi-domain] Cd Length: 216 Bit Score: 184.53 E-value: 7.39e-56
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
58-222
3.25e-23
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: 95.67 E-value: 3.25e-23
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
62-274
1.13e-17
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: 81.23 E-value: 1.13e-17
oxygen-independent coproporphyrinogen III oxidase; This model represents HemN, the ...
6-457
0e+00
oxygen-independent coproporphyrinogen III oxidase; This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]
Pssm-ID: 129629 [Multi-domain] Cd Length: 455 Bit Score: 772.81 E-value: 0e+00
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase ...
24-445
0e+00
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase [Coenzyme transport and metabolism]; Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase is part of the Pathway/BioSystem: Heme biosynthesis
Pssm-ID: 440400 [Multi-domain] Cd Length: 400 Bit Score: 512.03 E-value: 0e+00
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
52-270
7.39e-56
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Pssm-ID: 214792 [Multi-domain] Cd Length: 216 Bit Score: 184.53 E-value: 7.39e-56
putative heme utilization radical SAM enzyme HutW; HutW is a radical SAM enzyme closely ...
33-430
3.64e-43
putative heme utilization radical SAM enzyme HutW; HutW is a radical SAM enzyme closely related to HemN, the heme biosynthetic oxygen-independent coproporphyrinogen oxidase. It belongs to operons associated with heme uptake and utilization in Vibrio cholerae and related species, but neither it not HutX has been shown to be needed, as is HutZ, for heme utilization. HutW failed to complement a Salmonella enterica hemN mutant (), suggesting a related but distinct activity. Some members of this family are fused to hutX.
Pssm-ID: 274985 [Multi-domain] Cd Length: 420 Bit Score: 156.99 E-value: 3.64e-43
putative oxygen-independent coproporphyrinogen III oxidase; Experimentally determined examples ...
53-367
4.16e-43
putative oxygen-independent coproporphyrinogen III oxidase; Experimentally determined examples of oxygen-independent coproporphyrinogen III oxidase, an enzyme that replaces HemF function under anaerobic conditions, belong to a family of proteins described by the model hemN. This model, hemN_rel, models a closely related protein, shorter at the amino end and lacking the region containing the motif PYRT[SC]YP found in members of the hemN family. Several species, including E. coli, Helicobacter pylori, Aquifex aeolicus, and Chlamydia trachomatis, have members of both this family and the E. coli hemN family. The member of this family from Bacillus subtilis was shown to complement an hemF/hemN double mutant of Salmonella typimurium and to prevent accumulation of coproporphyrinogen III under anaerobic conditions, but the exact role of this protein is still uncertain. It is found in a number of species that do not synthesize heme de novo. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]
Pssm-ID: 129630 [Multi-domain] Cd Length: 360 Bit Score: 155.45 E-value: 4.16e-43
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
58-222
3.25e-23
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: 95.67 E-value: 3.25e-23
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
62-274
1.13e-17
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: 81.23 E-value: 1.13e-17
HemN C-terminal domain; Members of this family are all oxygen-independent ...
363-431
1.71e-08
HemN C-terminal domain; Members of this family are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyzes the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX, one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain (pfam04055) suggest it may be a substrate binding domain.
Pssm-ID: 462055 [Multi-domain] Cd Length: 66 Bit Score: 51.09 E-value: 1.71e-08
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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