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Conserved domains on  [gi|334186168|ref|NP_191660|]
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Ferritin/ribonucleotide reductase-like family protein [Arabidopsis thaliana]

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, ...
 369-418 3.78e-15

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 cd01056:

Pssm-ID: 469698  Cd Length: 161  Bit Score: 72.58  E-value: 3.78e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 334186168 369 IDVEYNVSYVYHALDAYIERDNVGLKGFTKFFNDSSLEERGYAEKFMEYQ 418
Cdd:cd01056   12 INLELNASYVYLSMAAYFDRDDVALPGFAKFFRKLSDEEREHAEKLIKYQ 61
Glyco_hydro_85 super family cl47832
Glycosyl hydrolase family 85; Family of endo-beta-N-acetylglucosaminidases. These enzymes work ...
 3-39 7.57e-07

Glycosyl hydrolase family 85; Family of endo-beta-N-acetylglucosaminidases. These enzymes work on a broad spectrum of substrates.


The actual alignment was detected with superfamily member pfam03644:

Pssm-ID: 461002  Cd Length: 292  Bit Score: 50.36  E-value: 7.57e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 334186168    3 LYLLKRNNVSAAMFAPGWVYETAQQ---PNFNSAQNKWWS 39
Cdd:pfam03644 211 LDLIAKAGLSAALFAPGWTYETFQSgstPDFLERERRFWV 250
 
Name Accession Description Interval E-value
Euk_Ferritin cd01056
eukaryotic ferritins; Eukaryotic Ferritin (Euk_Ferritin) domain. Ferritins are the primary ...
 369-418 3.78e-15

eukaryotic ferritins; Eukaryotic Ferritin (Euk_Ferritin) domain. Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the dinuclear ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite; the protein shell can hold up to 4500 iron atoms. In vertebrates, two types of chains (subunits) have been characterized, H or M (fast) and L (slow), which differ in rates of iron uptake and mineralization. Fe(II) oxidation in the H/M subunits take place initially at the ferroxidase center, a carboxylate-bridged diiron center, located within the subunit four-helix bundle. In a complementary role, negatively charged residues on the protein shell inner surface of the L subunits promote ferrihydrite nucleation. Most plant ferritins combine both oxidase and nucleation functions in one chain: they have four interior glutamate residues as well as seven ferroxidase center residues.


Pssm-ID: 153114  Cd Length: 161  Bit Score: 72.58  E-value: 3.78e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 334186168 369 IDVEYNVSYVYHALDAYIERDNVGLKGFTKFFNDSSLEERGYAEKFMEYQ 418
Cdd:cd01056   12 INLELNASYVYLSMAAYFDRDDVALPGFAKFFRKLSDEEREHAEKLIKYQ 61
Glyco_hydro_85 pfam03644
Glycosyl hydrolase family 85; Family of endo-beta-N-acetylglucosaminidases. These enzymes work ...
 3-39 7.57e-07

Glycosyl hydrolase family 85; Family of endo-beta-N-acetylglucosaminidases. These enzymes work on a broad spectrum of substrates.


Pssm-ID: 461002  Cd Length: 292  Bit Score: 50.36  E-value: 7.57e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 334186168    3 LYLLKRNNVSAAMFAPGWVYETAQQ---PNFNSAQNKWWS 39
Cdd:pfam03644 211 LDLIAKAGLSAALFAPGWTYETFQSgstPDFLERERRFWV 250
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 372-418 3.33e-06

Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins.


Pssm-ID: 459712  Cd Length: 141  Bit Score: 46.51  E-value: 3.33e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 334186168  372 EYNVSYVYHALDAYIerDNVGLKGFTKFFNDSSLEERGYAEKFMEYQ 418
Cdd:pfam00210  11 ELTASYQYLQMHWYV--KGPGFEGLHEFFDEQAEEEREHADKLAERI 55
GH85_ENGase cd06547
Endo-beta-N-acetylglucosaminidase (ENGase) hydrolyzes the N-N'-diacetylchitobiosyl core of ...
 5-58 4.53e-05

Endo-beta-N-acetylglucosaminidase (ENGase) hydrolyzes the N-N'-diacetylchitobiosyl core of N-glycosylproteins. The beta-1,4-glycosyl bond located between two N-acetylglucosamine residues is hydrolyzed such that N-acetylglucosamine 1 remains with the protein and N-acetylglucosamine 2 forms the reducing end of the released glycan. ENGase is a key enzyme in the processing of free oligosaccharides in the cytosol of eukaryotes. Oligosaccharides formed in the lumen of the endoplasmic reticulum are transported into the cytosol where they are catabolized by cytosolic ENGases and other enzymes, possibly to maximize the reutilization of the component sugars. ENGases have an eight-stranded alpha/beta barrel topology and are classified as a family 85 glycosyl hydrolase (GH85) domain. The GH85 ENGases are sequence-similar to the family 18 glycosyl hydrolases, also known as GH18 chitinases. An ENGase-like protein is also found in bacteria and is included in this alignment model.


Pssm-ID: 119364  Cd Length: 339  Bit Score: 45.37  E-value: 4.53e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334186168   5 LLKRNNVSAAMFAPGWVYETAQQPNF---------------NSAQNKWWSLVEKSCGIVQTIHKSSLFT 58
Cdd:cd06547  229 EIKKAGLSVALFAPGWTYESFEEPDFfvknesrfgesgdpfLTNDDKFWSGLATYVPEKSPITSLPFVT 297
FtnA COG1528
Ferritin [Inorganic ion transport and metabolism];
376-417 6.54e-04

Ferritin [Inorganic ion transport and metabolism];


Pssm-ID: 441137  Cd Length: 158  Bit Score: 40.11  E-value: 6.54e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 334186168 376 SYVYHALDAYIerDNVGLKGFTKFFNDSSLEERGYAEKFMEY 417
Cdd:COG1528   21 SYLYLAMAAWC--DEKGLPGFANFFRVQAQEERTHAMKFFDY 60
 
Name Accession Description Interval E-value
Euk_Ferritin cd01056
eukaryotic ferritins; Eukaryotic Ferritin (Euk_Ferritin) domain. Ferritins are the primary ...
 369-418 3.78e-15

eukaryotic ferritins; Eukaryotic Ferritin (Euk_Ferritin) domain. Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the dinuclear ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite; the protein shell can hold up to 4500 iron atoms. In vertebrates, two types of chains (subunits) have been characterized, H or M (fast) and L (slow), which differ in rates of iron uptake and mineralization. Fe(II) oxidation in the H/M subunits take place initially at the ferroxidase center, a carboxylate-bridged diiron center, located within the subunit four-helix bundle. In a complementary role, negatively charged residues on the protein shell inner surface of the L subunits promote ferrihydrite nucleation. Most plant ferritins combine both oxidase and nucleation functions in one chain: they have four interior glutamate residues as well as seven ferroxidase center residues.


Pssm-ID: 153114  Cd Length: 161  Bit Score: 72.58  E-value: 3.78e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 334186168 369 IDVEYNVSYVYHALDAYIERDNVGLKGFTKFFNDSSLEERGYAEKFMEYQ 418
Cdd:cd01056   12 INLELNASYVYLSMAAYFDRDDVALPGFAKFFRKLSDEEREHAEKLIKYQ 61
Ferritin cd00904
Ferritin iron storage proteins; Ferritins are the primary iron storage proteins of most living ...
 369-418 3.03e-09

Ferritin iron storage proteins; Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the dinuclear ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite; the protein shell can hold up to 4500 iron atoms. In vertebrates, two types of chains (subunits) have been characterized, H or M (fast) and L (slow), which differ in rates of iron uptake and mineralization. Bacterial non-heme ferritins are composed only of H chains. Fe(II) oxidation in the H/M subunits take place initially at the ferroxidase center, a carboxylate-bridged diiron center, located within the subunit four-helix bundle. In a complementary role, negatively charged residues on the protein shell inner surface of the L subunits promote ferrihydrite nucleation. Most plant ferritins combine both oxidase and nucleation functions in one chain: they have four interior glutamate residues as well as seven ferroxidase center residues.


Pssm-ID: 153098  Cd Length: 160  Bit Score: 55.73  E-value: 3.03e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 334186168 369 IDVEYNVSYVYHALDAYIERDNVGLKGFTKFFNDSSLEERGYAEKFMEYQ 418
Cdd:cd00904   12 LNLELYASYTYLSMATYFDRDDVALKGVAHFFKEQAQEEREHAEKFYKYQ 61
Glyco_hydro_85 pfam03644
Glycosyl hydrolase family 85; Family of endo-beta-N-acetylglucosaminidases. These enzymes work ...
 3-39 7.57e-07

Glycosyl hydrolase family 85; Family of endo-beta-N-acetylglucosaminidases. These enzymes work on a broad spectrum of substrates.


Pssm-ID: 461002  Cd Length: 292  Bit Score: 50.36  E-value: 7.57e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 334186168    3 LYLLKRNNVSAAMFAPGWVYETAQQ---PNFNSAQNKWWS 39
Cdd:pfam03644 211 LDLIAKAGLSAALFAPGWTYETFQSgstPDFLERERRFWV 250
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 372-418 3.33e-06

Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins.


Pssm-ID: 459712  Cd Length: 141  Bit Score: 46.51  E-value: 3.33e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 334186168  372 EYNVSYVYHALDAYIerDNVGLKGFTKFFNDSSLEERGYAEKFMEYQ 418
Cdd:pfam00210  11 ELTASYQYLQMHWYV--KGPGFEGLHEFFDEQAEEEREHADKLAERI 55
GH85_ENGase cd06547
Endo-beta-N-acetylglucosaminidase (ENGase) hydrolyzes the N-N'-diacetylchitobiosyl core of ...
 5-58 4.53e-05

Endo-beta-N-acetylglucosaminidase (ENGase) hydrolyzes the N-N'-diacetylchitobiosyl core of N-glycosylproteins. The beta-1,4-glycosyl bond located between two N-acetylglucosamine residues is hydrolyzed such that N-acetylglucosamine 1 remains with the protein and N-acetylglucosamine 2 forms the reducing end of the released glycan. ENGase is a key enzyme in the processing of free oligosaccharides in the cytosol of eukaryotes. Oligosaccharides formed in the lumen of the endoplasmic reticulum are transported into the cytosol where they are catabolized by cytosolic ENGases and other enzymes, possibly to maximize the reutilization of the component sugars. ENGases have an eight-stranded alpha/beta barrel topology and are classified as a family 85 glycosyl hydrolase (GH85) domain. The GH85 ENGases are sequence-similar to the family 18 glycosyl hydrolases, also known as GH18 chitinases. An ENGase-like protein is also found in bacteria and is included in this alignment model.


Pssm-ID: 119364  Cd Length: 339  Bit Score: 45.37  E-value: 4.53e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334186168   5 LLKRNNVSAAMFAPGWVYETAQQPNF---------------NSAQNKWWSLVEKSCGIVQTIHKSSLFT 58
Cdd:cd06547  229 EIKKAGLSVALFAPGWTYESFEEPDFfvknesrfgesgdpfLTNDDKFWSGLATYVPEKSPITSLPFVT 297
Nonheme_Ferritin cd01055
nonheme-containing ferritins; Nonheme Ferritin domain, found in archaea and bacteria, is a ...
 369-417 1.79e-04

nonheme-containing ferritins; Nonheme Ferritin domain, found in archaea and bacteria, is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The ferritin protein shell is composed of 24 protein subunits arranged in 432 symmetry. Each protein subunit, a four-helix bundle with a fifth short terminal helix, contains a dinuclear ferroxidase center (H type). Unique to this group of proteins is a third metal site in the ferroxidase center. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite.


Pssm-ID: 153113  Cd Length: 156  Bit Score: 41.70  E-value: 1.79e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 334186168 369 IDVEYNVSYVYHALDAYIerDNVGLKGFTKFFNDSSLEERGYAEKFMEY 417
Cdd:cd01055   12 INLELYSSYLYLAMAAWF--DSKGLDGFANFFRVQAQEEREHAMKFFDY 58
FtnA COG1528
Ferritin [Inorganic ion transport and metabolism];
376-417 6.54e-04

Ferritin [Inorganic ion transport and metabolism];


Pssm-ID: 441137  Cd Length: 158  Bit Score: 40.11  E-value: 6.54e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 334186168 376 SYVYHALDAYIerDNVGLKGFTKFFNDSSLEERGYAEKFMEY 417
Cdd:COG1528   21 SYLYLAMAAWC--DEKGLPGFANFFRVQAQEERTHAMKFFDY 60
 
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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