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Conserved domains on  [gi|2443672699|ref|WP_273271314|]
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tRNA-dihydrouridine synthase, partial [Methylophaga sp.]

Protein Classification

tRNA-dihydrouridine synthase( domain architecture ID 1000774)

tRNA-dihydrouridine synthase catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs

EC:  1.3.1.-
Gene Ontology:  GO:0008033

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
nifR3_yhdG super family cl31028
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 1-78 5.32e-22

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


The actual alignment was detected with superfamily member TIGR00737:

Pssm-ID: 129820  Cd Length: 319  Bit Score: 86.65  E-value: 5.32e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2443672699   1 YLEHDKLLSSPSVAEIRQILIEHLENLYDFYGDFSGVRMARKHIAWYSKGLRNGNAFRQEMNLLESPQQQVDFTRQFF 78
Cdd:TIGR00737 238 YLTTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIARKHIAWYLKGFPGNAALRQTLNHASSFQEVKQLLDDFF 315
 
Name Accession Description Interval E-value
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 1-78 5.32e-22

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


Pssm-ID: 129820  Cd Length: 319  Bit Score: 86.65  E-value: 5.32e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2443672699   1 YLEHDKLLSSPSVAEIRQILIEHLENLYDFYGDFSGVRMARKHIAWYSKGLRNGNAFRQEMNLLESPQQQVDFTRQFF 78
Cdd:TIGR00737 238 YLTTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIARKHIAWYLKGFPGNAALRQTLNHASSFQEVKQLLDDFF 315
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 11-72 3.89e-20

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: 81.68  E-value: 3.89e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2443672699  11 PSVAEIRQILIEHLENLYDFYGDFSGVRMARKHIAWYSKGLRNGNAFRQEMNLLESPQQQVD 72
Cdd:COG0042   246 PSLEEVLELLLEHLELLLEFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLE 307
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 1-81 2.35e-17

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 74.24  E-value: 2.35e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443672699   1 YLEHDKLLSSPSVAEIRQILIEHLENLYDFYGDFSGVRMARKHIAWYSKGLRNGNAFRQEMNLLESPQQQVDFTRQFFDQ 80
Cdd:PRK10415  240 YLDTGELLPPLPLAEVKRLLCAHVRELHDFYGPAKGYRIARKHVSWYLQEHAPNDQFRRTFNAIEDASEQLEALEAYFEN 319


                  .
gi 2443672699  81 L 81
Cdd:PRK10415  320 F 320
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 1-79 1.79e-15

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: 68.89  E-value: 1.79e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2443672699   1 YLEHDKLLSSPSVAEIRQILIEHLENLYDFYGDFSGVRMARKHIAWYSKGLRNGNAFRQEMNLLESPQQQVDFTRQFFD 79
Cdd:pfam01207 228 TVKTGEFGPSPPLAEEAEKVLRHLPYLEEFLGEDKGLRHARKHLAWYLKGFPGAAELRRELNDVFDPVEALINLDAALR 306
 
Name Accession Description Interval E-value
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 1-78 5.32e-22

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


Pssm-ID: 129820  Cd Length: 319  Bit Score: 86.65  E-value: 5.32e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2443672699   1 YLEHDKLLSSPSVAEIRQILIEHLENLYDFYGDFSGVRMARKHIAWYSKGLRNGNAFRQEMNLLESPQQQVDFTRQFF 78
Cdd:TIGR00737 238 YLTTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIARKHIAWYLKGFPGNAALRQTLNHASSFQEVKQLLDDFF 315
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 11-72 3.89e-20

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: 81.68  E-value: 3.89e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2443672699  11 PSVAEIRQILIEHLENLYDFYGDFSGVRMARKHIAWYSKGLRNGNAFRQEMNLLESPQQQVD 72
Cdd:COG0042   246 PSLEEVLELLLEHLELLLEFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLE 307
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 1-81 2.35e-17

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 74.24  E-value: 2.35e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443672699   1 YLEHDKLLSSPSVAEIRQILIEHLENLYDFYGDFSGVRMARKHIAWYSKGLRNGNAFRQEMNLLESPQQQVDFTRQFFDQ 80
Cdd:PRK10415  240 YLDTGELLPPLPLAEVKRLLCAHVRELHDFYGPAKGYRIARKHVSWYLQEHAPNDQFRRTFNAIEDASEQLEALEAYFEN 319


                  .
gi 2443672699  81 L 81
Cdd:PRK10415  320 F 320
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 1-79 1.79e-15

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: 68.89  E-value: 1.79e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2443672699   1 YLEHDKLLSSPSVAEIRQILIEHLENLYDFYGDFSGVRMARKHIAWYSKGLRNGNAFRQEMNLLESPQQQVDFTRQFFD 79
Cdd:pfam01207 228 TVKTGEFGPSPPLAEEAEKVLRHLPYLEEFLGEDKGLRHARKHLAWYLKGFPGAAELRRELNDVFDPVEALINLDAALR 306
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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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