CofD/YvcK family protein similar to Bacillus subtilis gluconeogenesis factor YvcK, which is essential for growth on intermediates of the Krebs cycle and the pentose phosphate pathway and may play a role in carbon metabolism, and related to CofD, a 2-phospho-L-lactate transferase involved in F420 biosynthesis
Family of CofD-like proteins and proteins related to YvcK; CofD is a 2-phospho-L-lactate ...
2-322
1.27e-121
Family of CofD-like proteins and proteins related to YvcK; CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. YvcK from Bacillus subtilis is a member of a family of mostly uncharacterized proteins and has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and pentose phosphate pathway. Both families appear to have a conserved phosphate binding site, but have different substrate binding residues conserved within each family.
The actual alignment was detected with superfamily member cd07186:
Pssm-ID: 444899 Cd Length: 303 Bit Score: 351.51 E-value: 1.27e-121
LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis; CofD is a ...
2-322
1.27e-121
LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis; CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis.
Pssm-ID: 132872 Cd Length: 303 Bit Score: 351.51 E-value: 1.27e-121
2-phospho-L-lactate transferase; This model represents LPPG:Fo 2-phospho-L-lactate transferase, ...
3-322
5.40e-117
2-phospho-L-lactate transferase; This model represents LPPG:Fo 2-phospho-L-lactate transferase, which catalyses the fourth step in the biosynthesis of coenzyme F420, a flavin derivative found in methanogens, the Mycobacteria, and several other lineages. This enzyme is characterized so far in Methanococcus jannaschii but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. The clade represented by this model is one of two major divisions of proteins in pfam01933. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 130878 Cd Length: 297 Bit Score: 339.80 E-value: 5.40e-117
Archaeal 2-phospho-L-lactate transferase/Bacterial gluconeogenesis factor, CofD/UPF0052 family ...
1-323
1.18e-44
Archaeal 2-phospho-L-lactate transferase/Bacterial gluconeogenesis factor, CofD/UPF0052 family [Carbohydrate transport and metabolism, Coenzyme transport and metabolism];
Pssm-ID: 440160 Cd Length: 314 Bit Score: 154.91 E-value: 1.18e-44
2-phospho-L-lactate transferase CofD; This entry contains 2-phospho-L-lactate transferase ...
2-270
2.16e-38
2-phospho-L-lactate transferase CofD; This entry contains 2-phospho-L-lactate transferase (CofD), phosphoenolpyruvate transferase and related sequences. CofD catalyzes the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2)diphospho-(5') guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl- 8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterized so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. CofD monomer contains 12 beta- strands, seven of them form a Rossmann fold, and 13 alpha-helices.
Pssm-ID: 426519 Cd Length: 249 Bit Score: 136.42 E-value: 2.16e-38
LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis; CofD is a ...
2-322
1.27e-121
LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis; CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis.
Pssm-ID: 132872 Cd Length: 303 Bit Score: 351.51 E-value: 1.27e-121
2-phospho-L-lactate transferase; This model represents LPPG:Fo 2-phospho-L-lactate transferase, ...
3-322
5.40e-117
2-phospho-L-lactate transferase; This model represents LPPG:Fo 2-phospho-L-lactate transferase, which catalyses the fourth step in the biosynthesis of coenzyme F420, a flavin derivative found in methanogens, the Mycobacteria, and several other lineages. This enzyme is characterized so far in Methanococcus jannaschii but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. The clade represented by this model is one of two major divisions of proteins in pfam01933. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 130878 Cd Length: 297 Bit Score: 339.80 E-value: 5.40e-117
Archaeal 2-phospho-L-lactate transferase/Bacterial gluconeogenesis factor, CofD/UPF0052 family ...
1-323
1.18e-44
Archaeal 2-phospho-L-lactate transferase/Bacterial gluconeogenesis factor, CofD/UPF0052 family [Carbohydrate transport and metabolism, Coenzyme transport and metabolism];
Pssm-ID: 440160 Cd Length: 314 Bit Score: 154.91 E-value: 1.18e-44
2-phospho-L-lactate transferase CofD; This entry contains 2-phospho-L-lactate transferase ...
2-270
2.16e-38
2-phospho-L-lactate transferase CofD; This entry contains 2-phospho-L-lactate transferase (CofD), phosphoenolpyruvate transferase and related sequences. CofD catalyzes the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2)diphospho-(5') guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl- 8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterized so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. CofD monomer contains 12 beta- strands, seven of them form a Rossmann fold, and 13 alpha-helices.
Pssm-ID: 426519 Cd Length: 249 Bit Score: 136.42 E-value: 2.16e-38
Family of CofD-like proteins and proteins related to YvcK; CofD is a 2-phospho-L-lactate ...
2-294
9.26e-29
Family of CofD-like proteins and proteins related to YvcK; CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. YvcK from Bacillus subtilis is a member of a family of mostly uncharacterized proteins and has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and pentose phosphate pathway. Both families appear to have a conserved phosphate binding site, but have different substrate binding residues conserved within each family.
Pssm-ID: 132871 Cd Length: 309 Bit Score: 112.68 E-value: 9.26e-29
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.
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