Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, ...
11-746
0e+00
Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate in which two cysteines and one glycine form radicals that are required for catalysis. PFL has a ten-stranded alpha/beta barrel domain that is structurally similar to those of all three ribonucleotide reductase (RNR) classes as well as benzylsuccinate synthase and B12-independent glycerol dehydratase.
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Pssm-ID: 153087 [Multi-domain] Cd Length: 738 Bit Score: 1527.30 E-value: 0e+00
Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, ...
11-746
0e+00
Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate in which two cysteines and one glycine form radicals that are required for catalysis. PFL has a ten-stranded alpha/beta barrel domain that is structurally similar to those of all three ribonucleotide reductase (RNR) classes as well as benzylsuccinate synthase and B12-independent glycerol dehydratase.
Pssm-ID: 153087 [Multi-domain] Cd Length: 738 Bit Score: 1527.30 E-value: 0e+00
formate acetyltransferase 1; Alternate names: pyruvate formate-lyase; formate C-acetyltransferase This enzyme converts formate + acetyl-CoA into pyruvate + CoA. This model describes formate acetyltransferase 1. More distantly related putative formate acetyltransferases have also been identified, including formate acetyltransferase 2 from E. coli, which is excluded from this model. [Energy metabolism, Fermentation]
Pssm-ID: 273525 [Multi-domain] Cd Length: 744 Bit Score: 1201.28 E-value: 0e+00
Pyruvate formate lyase-like; This family of enzymes includes pyruvate formate lyase, choline ...
23-608
0e+00
Pyruvate formate lyase-like; This family of enzymes includes pyruvate formate lyase, choline trimethylamine lyase, glycerol dehydratase, 4-hydroxyphenylacetate decarboxylase, and benzylsuccinate synthase.
Pssm-ID: 427048 Cd Length: 647 Bit Score: 771.42 E-value: 0e+00
autonomous glycyl radical cofactor GrcA3; This small protein, like GrcA and GrcA2, is a ...
674-749
3.92e-42
autonomous glycyl radical cofactor GrcA3; This small protein, like GrcA and GrcA2, is a lineage-specific small protein related to the glycyl radical active site-containing C-terminal region of pyruvate formate-lyase (PFL, also called formate C-acetyltransferase) from similar species. Because PFL is prone to damage and inactivation, this protein is made as a spare part that fills in for the portion of the protein that was damaged and lost. The distinct families we now call GrcA, GrcA2, and GrcA3 all have the surprising property of being much more closely related to some full length PFL than to members of the other GrcA-series families.
Pssm-ID: 439653 [Multi-domain] Cd Length: 78 Bit Score: 147.58 E-value: 3.92e-42
Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, ...
11-746
0e+00
Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate in which two cysteines and one glycine form radicals that are required for catalysis. PFL has a ten-stranded alpha/beta barrel domain that is structurally similar to those of all three ribonucleotide reductase (RNR) classes as well as benzylsuccinate synthase and B12-independent glycerol dehydratase.
Pssm-ID: 153087 [Multi-domain] Cd Length: 738 Bit Score: 1527.30 E-value: 0e+00
formate acetyltransferase 1; Alternate names: pyruvate formate-lyase; formate C-acetyltransferase This enzyme converts formate + acetyl-CoA into pyruvate + CoA. This model describes formate acetyltransferase 1. More distantly related putative formate acetyltransferases have also been identified, including formate acetyltransferase 2 from E. coli, which is excluded from this model. [Energy metabolism, Fermentation]
Pssm-ID: 273525 [Multi-domain] Cd Length: 744 Bit Score: 1201.28 E-value: 0e+00
Pyruvate formate lyase-like; This family of enzymes includes pyruvate formate lyase, choline ...
23-608
0e+00
Pyruvate formate lyase-like; This family of enzymes includes pyruvate formate lyase, choline trimethylamine lyase, glycerol dehydratase, 4-hydroxyphenylacetate decarboxylase, and benzylsuccinate synthase.
Pssm-ID: 427048 Cd Length: 647 Bit Score: 771.42 E-value: 0e+00
Pyruvate formate lyase 2 and related enzymes; This family includes pyruvate formate lyase 2 ...
129-745
2.29e-89
Pyruvate formate lyase 2 and related enzymes; This family includes pyruvate formate lyase 2 (PFL2), B12-independent glycerol dehydratase (DhaB) and the alpha subunit of benzylsuccinate synthase (BssA), all of which have a highly conserved ten-stranded alpha/beta barrel domain, which is similar to those of PFL1 (pyruvate formate lyase 1) and RNR (ribonucleotide reductase). Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. DhaB catalyzes the first step in the conversion of glycerol to 1,3-propanediol while BssA catalyzes the first step in the anaerobic mineralization of both toluene and m-xylene.
Pssm-ID: 153086 [Multi-domain] Cd Length: 781 Bit Score: 297.27 E-value: 2.29e-89
Ribonucleotide reductase and Pyruvate formate lyase; Ribonucleotide reductase (RNR) and ...
154-699
8.84e-56
Ribonucleotide reductase and Pyruvate formate lyase; Ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL) are believed to have diverged from a common ancestor. They have a structurally similar ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs use a diiron-tyrosyl radical while Class II RNRs use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. PFL, an essential enzyme in anaerobic bacteria, catalyzes the conversion of pyruvate and CoA to acteylCoA and formate in a mechanism that uses a glycyl radical.
Pssm-ID: 153083 [Multi-domain] Cd Length: 401 Bit Score: 196.60 E-value: 8.84e-56
autonomous glycyl radical cofactor GrcA3; This small protein, like GrcA and GrcA2, is a ...
674-749
3.92e-42
autonomous glycyl radical cofactor GrcA3; This small protein, like GrcA and GrcA2, is a lineage-specific small protein related to the glycyl radical active site-containing C-terminal region of pyruvate formate-lyase (PFL, also called formate C-acetyltransferase) from similar species. Because PFL is prone to damage and inactivation, this protein is made as a spare part that fills in for the portion of the protein that was damaged and lost. The distinct families we now call GrcA, GrcA2, and GrcA3 all have the surprising property of being much more closely related to some full length PFL than to members of the other GrcA-series families.
Pssm-ID: 439653 [Multi-domain] Cd Length: 78 Bit Score: 147.58 E-value: 3.92e-42
choline trimethylamine-lyase; Members of this family, homologs to pyruvate formate-lyases and ...
198-747
3.10e-35
choline trimethylamine-lyase; Members of this family, homologs to pyruvate formate-lyases and benzylsuccinate synthases, are glycine radical enzymes that appear to act as choline TMA-lyase, that is, to perform a C-N bond cleavage turning choline into trimethylamine (TMA) plus acetaldehyde. The gene symbol is cutC, for choline utilization. The activase, CutD, is a radical SAM enzyme. [Energy metabolism, Amino acids and amines]
Pssm-ID: 275187 [Multi-domain] Cd Length: 789 Bit Score: 143.40 E-value: 3.10e-35
autonomous glycyl radical cofactor GrcA; This small protein, previously designated YfiD in E. ...
688-749
2.60e-26
autonomous glycyl radical cofactor GrcA; This small protein, previously designated YfiD in E. coli, is closely homologous to pyruvate formate_lyase (PFL) in a region surrounding the stable glycyl radical that is prepared by the action of pyruvate formate-lyase activase, a radical SAM enzyme. When damage at the site of this radical breaks the main chain of PFL, this protein acts as a spare part that reintroduces the needed stable glycyl radical. Cutoffs for this model are set to exclude a set of closely related phage proteins that appear to have a corresponding function.
Pssm-ID: 213978 [Multi-domain] Cd Length: 124 Bit Score: 104.50 E-value: 2.60e-26
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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(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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