class 1b ribonucleoside-diphosphate reductase subunit beta is the small subunit of the tetrameric enzyme, composed of two alpha and two beta subunits, that catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
ribonucleoside-diphosphate reductase, class 1b, beta subunit; Members of this family are NrdF, ...
12-325
0e+00
ribonucleoside-diphosphate reductase, class 1b, beta subunit; Members of this family are NrdF, the beta subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]
:
Pssm-ID: 275027 Cd Length: 313 Bit Score: 609.17 E-value: 0e+00
ribonucleoside-diphosphate reductase, class 1b, beta subunit; Members of this family are NrdF, ...
12-325
0e+00
ribonucleoside-diphosphate reductase, class 1b, beta subunit; Members of this family are NrdF, the beta subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]
Pssm-ID: 275027 Cd Length: 313 Bit Score: 609.17 E-value: 0e+00
Ribonucleotide reductase beta subunit, ferritin-like domain [Nucleotide transport and ...
5-322
1.54e-142
Ribonucleotide reductase beta subunit, ferritin-like domain [Nucleotide transport and metabolism]; Ribonucleotide reductase beta subunit, ferritin-like domain is part of the Pathway/BioSystem: Pyrimidine salvage
Pssm-ID: 439978 [Multi-domain] Cd Length: 326 Bit Score: 405.32 E-value: 1.54e-142
Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-helical bundle; some have 2 addition beta strands. Yeast is unique in that it assembles both homodimers and heterodimers of RNRR2. The yeast heterodimer, Y2Y4, contains R2 (Y2) and a R2 homolog (Y4) that lacks the diiron center and is proposed to only assist in cofactor assembly, and perhaps stabilize R1 (Y1) in its active conformation.
Pssm-ID: 153108 [Multi-domain] Cd Length: 288 Bit Score: 303.01 E-value: 9.30e-103
ribonucleoside-diphosphate reductase, class 1b, beta subunit; Members of this family are NrdF, ...
12-325
0e+00
ribonucleoside-diphosphate reductase, class 1b, beta subunit; Members of this family are NrdF, the beta subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]
Pssm-ID: 275027 Cd Length: 313 Bit Score: 609.17 E-value: 0e+00
Ribonucleotide reductase beta subunit, ferritin-like domain [Nucleotide transport and ...
5-322
1.54e-142
Ribonucleotide reductase beta subunit, ferritin-like domain [Nucleotide transport and metabolism]; Ribonucleotide reductase beta subunit, ferritin-like domain is part of the Pathway/BioSystem: Pyrimidine salvage
Pssm-ID: 439978 [Multi-domain] Cd Length: 326 Bit Score: 405.32 E-value: 1.54e-142
Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-helical bundle; some have 2 addition beta strands. Yeast is unique in that it assembles both homodimers and heterodimers of RNRR2. The yeast heterodimer, Y2Y4, contains R2 (Y2) and a R2 homolog (Y4) that lacks the diiron center and is proposed to only assist in cofactor assembly, and perhaps stabilize R1 (Y1) in its active conformation.
Pssm-ID: 153108 [Multi-domain] Cd Length: 288 Bit Score: 303.01 E-value: 9.30e-103
Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, ...
75-201
5.41e-03
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).
Pssm-ID: 153097 Cd Length: 130 Bit Score: 36.71 E-value: 5.41e-03
Ribonucleotide Reductase R2-like protein, Mn/Fe-binding domain; Rv0233 is a Mycobacterium ...
15-201
5.72e-03
Ribonucleotide Reductase R2-like protein, Mn/Fe-binding domain; Rv0233 is a Mycobacterium tuberculosis ribonucleotide reductase R2 protein with a heterodinuclear manganese/iron-carboxylate cofactor located in its metal center. The Rv0233-like family may represent a structural/functional counterpart of the evolutionary ancestor of the RNRR2's (Ribonucleotide Reductase, R2/beta subunit) and the bacterial multicomponent monooxygenases. RNRR2s belong to a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in prokaryotes and archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites.
Pssm-ID: 153120 Cd Length: 280 Bit Score: 37.71 E-value: 5.72e-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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