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Conserved domains on  [gi|2747583661|ref|WP_350669767|]
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tRNA isopentenyl-2-thiomethyl-A-37 hydroxylase MiaE, partial [Pseudoalteromonas sp. 43-MNA-CIBAN-0464]

Protein Classification

ferritin family protein( domain architecture ID 38)

ferritin family protein similar to rubrerythrin, a non-heme di-iron that is involved in oxidative stress defense as a peroxide scavenger in a wide range of organisms

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ferritin_like super family cl00264
Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, ...
 37-76 5.48e-14

Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF).


The actual alignment was detected with superfamily member pfam06175:

Pssm-ID: 469698  Cd Length: 199  Bit Score: 63.26  E-value: 5.48e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2747583661  37 SPYGQDLIDKMVMLIKEELHHFYQVLEIMDEYGVEYKSIT 76
Cdd:pfam06175  54 APSNQDLVNKLTRLAKEELHHFEQVLEILEARNIPYAPIS 93
 
Name Accession Description Interval E-value
MiaE pfam06175
tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE); This family consists of several bacterial tRNA-(MS(2)IO ...
 37-76 5.48e-14

tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE); This family consists of several bacterial tRNA-(MS(2)IO(6)A)-hydroxylase (MiaE) proteins. The modified nucleoside 2-methylthio-N-6-isopentenyl adenosine (ms2i6A) is present at position 37 (3' of the anticodon) of tRNAs that read codons beginning with U except tRNA(I,V Ser) in Escherichia coli. Salmonella typhimurium 2-methylthio-cis-ribozeatin (ms2io6A) is found in tRNA, probably in the corresponding species that have ms2i6A in E. coli. The miaE gene is absent in E. coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species.


Pssm-ID: 114868  Cd Length: 199  Bit Score: 63.26  E-value: 5.48e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2747583661  37 SPYGQDLIDKMVMLIKEELHHFYQVLEIMDEYGVEYKSIT 76
Cdd:pfam06175  54 APSNQDLVNKLTRLAKEELHHFEQVLEILEARNIPYAPIS 93
MiaE cd07910
MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; MiaE is ...
 42-76 5.79e-07

MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; MiaE is a nonheme diiron monooxygenase that catalyzes the posttranscriptional allylic hydroxylation of a modified nucleoside in tRNA called 2-methylthio-N-6-isopentenyl adenosine (ms2i6A). ms2i6A is found at position 37, next to the anticodon at the 3' position in almost all eukaryotic and bacterial tRNA's that read codons beginning with uridine. The miaE gene is absent in Escherichia coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species.


Pssm-ID: 153119  Cd Length: 180  Bit Score: 44.09  E-value: 5.79e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2747583661  42 DLIDKMVMLIKEELHHFYQVLEIMDEYGVEYKSIT 76
Cdd:cd07910    49 ELVEAMSDLAREELQHFEQVLKIMKKRGIPLGPDS 83
 
Name Accession Description Interval E-value
MiaE pfam06175
tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE); This family consists of several bacterial tRNA-(MS(2)IO ...
 37-76 5.48e-14

tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE); This family consists of several bacterial tRNA-(MS(2)IO(6)A)-hydroxylase (MiaE) proteins. The modified nucleoside 2-methylthio-N-6-isopentenyl adenosine (ms2i6A) is present at position 37 (3' of the anticodon) of tRNAs that read codons beginning with U except tRNA(I,V Ser) in Escherichia coli. Salmonella typhimurium 2-methylthio-cis-ribozeatin (ms2io6A) is found in tRNA, probably in the corresponding species that have ms2i6A in E. coli. The miaE gene is absent in E. coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species.


Pssm-ID: 114868  Cd Length: 199  Bit Score: 63.26  E-value: 5.48e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2747583661  37 SPYGQDLIDKMVMLIKEELHHFYQVLEIMDEYGVEYKSIT 76
Cdd:pfam06175  54 APSNQDLVNKLTRLAKEELHHFEQVLEILEARNIPYAPIS 93
MiaE cd07910
MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; MiaE is ...
 42-76 5.79e-07

MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; MiaE is a nonheme diiron monooxygenase that catalyzes the posttranscriptional allylic hydroxylation of a modified nucleoside in tRNA called 2-methylthio-N-6-isopentenyl adenosine (ms2i6A). ms2i6A is found at position 37, next to the anticodon at the 3' position in almost all eukaryotic and bacterial tRNA's that read codons beginning with uridine. The miaE gene is absent in Escherichia coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species.


Pssm-ID: 153119  Cd Length: 180  Bit Score: 44.09  E-value: 5.79e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2747583661  42 DLIDKMVMLIKEELHHFYQVLEIMDEYGVEYKSIT 76
Cdd:cd07910    49 ELVEAMSDLAREELQHFEQVLKIMKKRGIPLGPDS 83
 
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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