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Conserved domains on  [gi|1113485281|gb|OJX46247|]
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DNA starvation/stationary phase protection protein Dps [Chloroflexi bacterium 44-23]

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, ...
 9-166 3.07e-63

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 PRK09448:

Pssm-ID: 469698  Cd Length: 162  Bit Score: 191.74  E-value: 3.07e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281   9 KIFPTQVDIPERNRERVIDLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAK 88
Cdd:PRK09448    7 NLLYTRNDVPDSEKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVAL 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1113485281  89 GTSRMAADSSQVEEFP-DVNSGMEVVHALIERYGVVANCMREDIDEtekLEDMGTNDLFIEITRVLDKALYFLESHIQD 166
Cdd:PRK09448   87 GTTQVVASKTPLKSYPlDIHNVQDHLKALADRYAIVANDVRKAIDE---AGDEDTADIFTAASRDLDKFLWFIEAHIEE 162
 
Name Accession Description Interval E-value
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 9-166 3.07e-63

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 191.74  E-value: 3.07e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281   9 KIFPTQVDIPERNRERVIDLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAK 88
Cdd:PRK09448    7 NLLYTRNDVPDSEKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVAL 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1113485281  89 GTSRMAADSSQVEEFP-DVNSGMEVVHALIERYGVVANCMREDIDEtekLEDMGTNDLFIEITRVLDKALYFLESHIQD 166
Cdd:PRK09448   87 GTTQVVASKTPLKSYPlDIHNVQDHLKALADRYAIVANDVRKAIDE---AGDEDTADIFTAASRDLDKFLWFIEAHIEE 162
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 12-166 2.64e-56

DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism, Defense mechanisms];


Pssm-ID: 440546 [Multi-domain]  Cd Length: 156  Bit Score: 173.87  E-value: 2.64e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281  12 PTQVDIPERNRERVIDLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAKGTS 91
Cdd:COG0783     1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1113485281  92 RMAADSSQVEEFP-DVNSGMEVVHALIERYGVVANCMREDIDETEKLEDMGTNDLFIEITRVLDKALYFLESHIQD 166
Cdd:COG0783    81 AEFAKLSTIKEEPeGVVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHLED 156
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 27-164 8.06e-48

DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation. Members of the DPS family are homopolymers formed by 12 four-helix bundle subunits that assemble with 23 symmetry into a hollow shell. The DPS ferroxidase site is unusual in that it is not located in a four-helix bundle as in ferritin, but is shared by 2-fold symmetry-related subunits providing the iron ligands. Many DPS sequences (e.g., E. coli) display an N-terminal extension of variable length that contains two or three positively charged lysine residues that extends into the solvent and is thought to play an important role in the stabilization of the complex with DNA. DPS Listeria Flp, Bacillus anthracis Dlp-1 and Dlp-2, and Helicobacter pylori HP-NAP which lack the N-terminal extension, do not bind DNA. DPS proteins from Helicobacter pylori, Treponema pallidum, and Borrelia burgdorferi are highly immunogenic.


Pssm-ID: 153102  Cd Length: 139  Bit Score: 151.54  E-value: 8.06e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281  27 DLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAKGTSRMAADSSQVEEFP-D 105
Cdd:cd01043     1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPaG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1113485281 106 VNSGMEVVHALIERYGVVANCMREDIDETEKLEDMGTNDLFIEITRVLDKALYFLESHI 164
Cdd:cd01043    81 VLSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAHL 139
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 26-166 4.35e-24

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: 91.19  E-value: 4.35e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281  26 IDLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAKGTsrmAADSSQVEEFPD 105
Cdd:pfam00210   1 IAALNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGT---RVELLAIEAPPS 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1113485281 106 VNSGMEVVHALIERYGVVANCMREDIDETEKLEDMGTNDLFIEITRVLDKALYFLESHIQD 166
Cdd:pfam00210  78 FGSVLEVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEALLEK 138
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
23-149 3.54e-17

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 74.22  E-value: 3.54e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281  23 ERVIDLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAKGTSRMAADSSQVE- 101
Cdd:NF041388   22 EQIVDALNTDLAATYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQALGGVPVSGPAALEEHAPVEp 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1113485281 102 EFPDVNSGMEVVHALIERYGVVANCMREDIDETEKLEDMGTNDLFIEI 149
Cdd:NF041388  102 EGEDVYDIRTSLENDLEMYGDIIESVRDHIELAENLGDHATAELLREQ 149
 
Name Accession Description Interval E-value
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 9-166 3.07e-63

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 191.74  E-value: 3.07e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281   9 KIFPTQVDIPERNRERVIDLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAK 88
Cdd:PRK09448    7 NLLYTRNDVPDSEKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVAL 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1113485281  89 GTSRMAADSSQVEEFP-DVNSGMEVVHALIERYGVVANCMREDIDEtekLEDMGTNDLFIEITRVLDKALYFLESHIQD 166
Cdd:PRK09448   87 GTTQVVASKTPLKSYPlDIHNVQDHLKALADRYAIVANDVRKAIDE---AGDEDTADIFTAASRDLDKFLWFIEAHIEE 162
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 12-166 2.64e-56

DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism, Defense mechanisms];


Pssm-ID: 440546 [Multi-domain]  Cd Length: 156  Bit Score: 173.87  E-value: 2.64e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281  12 PTQVDIPERNRERVIDLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAKGTS 91
Cdd:COG0783     1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1113485281  92 RMAADSSQVEEFP-DVNSGMEVVHALIERYGVVANCMREDIDETEKLEDMGTNDLFIEITRVLDKALYFLESHIQD 166
Cdd:COG0783    81 AEFAKLSTIKEEPeGVVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHLED 156
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 27-164 8.06e-48

DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation. Members of the DPS family are homopolymers formed by 12 four-helix bundle subunits that assemble with 23 symmetry into a hollow shell. The DPS ferroxidase site is unusual in that it is not located in a four-helix bundle as in ferritin, but is shared by 2-fold symmetry-related subunits providing the iron ligands. Many DPS sequences (e.g., E. coli) display an N-terminal extension of variable length that contains two or three positively charged lysine residues that extends into the solvent and is thought to play an important role in the stabilization of the complex with DNA. DPS Listeria Flp, Bacillus anthracis Dlp-1 and Dlp-2, and Helicobacter pylori HP-NAP which lack the N-terminal extension, do not bind DNA. DPS proteins from Helicobacter pylori, Treponema pallidum, and Borrelia burgdorferi are highly immunogenic.


Pssm-ID: 153102  Cd Length: 139  Bit Score: 151.54  E-value: 8.06e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281  27 DLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAKGTSRMAADSSQVEEFP-D 105
Cdd:cd01043     1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPaG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1113485281 106 VNSGMEVVHALIERYGVVANCMREDIDETEKLEDMGTNDLFIEITRVLDKALYFLESHI 164
Cdd:cd01043    81 VLSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAHL 139
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 26-166 4.35e-24

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: 91.19  E-value: 4.35e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281  26 IDLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAKGTsrmAADSSQVEEFPD 105
Cdd:pfam00210   1 IAALNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGT---RVELLAIEAPPS 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1113485281 106 VNSGMEVVHALIERYGVVANCMREDIDETEKLEDMGTNDLFIEITRVLDKALYFLESHIQD 166
Cdd:pfam00210  78 FGSVLEVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEALLEK 138
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
23-149 3.54e-17

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 74.22  E-value: 3.54e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1113485281  23 ERVIDLLNQSLADIFDLHSQTKHAHWNVKGTDFYQLHILFDELAEMIFPYVDTIAERITALGGFAKGTSRMAADSSQVE- 101
Cdd:NF041388   22 EQIVDALNTDLAATYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQALGGVPVSGPAALEEHAPVEp 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1113485281 102 EFPDVNSGMEVVHALIERYGVVANCMREDIDETEKLEDMGTNDLFIEI 149
Cdd:NF041388  102 EGEDVYDIRTSLENDLEMYGDIIESVRDHIELAENLGDHATAELLREQ 149
 
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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