Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
65-395
8.40e-142
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.
The actual alignment was detected with superfamily member PRK11815:
Pssm-ID: 481211 [Multi-domain] Cd Length: 333 Bit Score: 406.83 E-value: 8.40e-142
tRNA dihydrouridine synthase A; This model represents one branch of COG0042 (Predicted ...
65-389
4.61e-99
tRNA dihydrouridine synthase A; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). It represents a distinct subset by a set of shared unique motifs, a conserved pattern of insertions/deletions relative to other nifR3 homologs, and by subclustering based on cross-genome bidirectional best hits. Members are found in species as diverse as the proteobacteria, a spirochete, a cyanobacterium, and Deinococcus radiodurans. NifR3 itself, a protein of unknown function associated with nitrogen regulation in Rhodobacter capsulatus, is not a member of this branch. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 129825 Cd Length: 318 Bit Score: 297.89 E-value: 4.61e-99
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
57-382
5.82e-91
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 439812 [Multi-domain] Cd Length: 310 Bit Score: 276.59 E-value: 5.82e-91
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
65-298
3.83e-82
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.
Pssm-ID: 239200 [Multi-domain] Cd Length: 231 Bit Score: 251.26 E-value: 3.83e-82
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
66-393
1.38e-62
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.
Pssm-ID: 426126 Cd Length: 309 Bit Score: 203.71 E-value: 1.38e-62
tRNA dihydrouridine synthase A; This model represents one branch of COG0042 (Predicted ...
65-389
4.61e-99
tRNA dihydrouridine synthase A; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). It represents a distinct subset by a set of shared unique motifs, a conserved pattern of insertions/deletions relative to other nifR3 homologs, and by subclustering based on cross-genome bidirectional best hits. Members are found in species as diverse as the proteobacteria, a spirochete, a cyanobacterium, and Deinococcus radiodurans. NifR3 itself, a protein of unknown function associated with nitrogen regulation in Rhodobacter capsulatus, is not a member of this branch. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 129825 Cd Length: 318 Bit Score: 297.89 E-value: 4.61e-99
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
57-382
5.82e-91
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 439812 [Multi-domain] Cd Length: 310 Bit Score: 276.59 E-value: 5.82e-91
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
65-298
3.83e-82
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.
Pssm-ID: 239200 [Multi-domain] Cd Length: 231 Bit Score: 251.26 E-value: 3.83e-82
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
66-393
1.38e-62
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.
Pssm-ID: 426126 Cd Length: 309 Bit Score: 203.71 E-value: 1.38e-62
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
120-194
1.46e-05
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.
Pssm-ID: 240091 [Multi-domain] Cd Length: 296 Bit Score: 46.39 E-value: 1.46e-05
Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate ...
107-194
2.37e-03
Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate dehydrogenase is part of the Pathway/BioSystem: Pyrimidine biosynthesis
Pssm-ID: 439937 [Multi-domain] Cd Length: 296 Bit Score: 39.67 E-value: 2.37e-03
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
120-203
6.94e-03
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.
Pssm-ID: 239204 [Multi-domain] Cd Length: 289 Bit Score: 38.10 E-value: 6.94e-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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