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Conserved domains on  [gi|1909714243|ref|WP_190596130|]
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MULTISPECIES: Dps family protein [Synechocystis]

Protein Classification

Dps family protein( domain architecture ID 10002504)

Dps family protein similar to DNA starvation/stationary phase protection protein that binds and protects DNA from cleavage caused by reactive oxygen species

CATH:  1.20.1260.10
Gene Ontology:  GO:0016491|GO:0008199
SCOP:  4000839

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 3-156 7.66e-73

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: 215.08  E-value: 7.66e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1909714243   3 TINIGIPEADRVKIAESLKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSLDVFAPGTY 82
Cdd:COG0783     1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1909714243  83 KEFSKLSSVQEVD-GIPTSKEMVDILTKGHETIVQSCRDVLKFSQPADDESTIALASDRMRVHEKTAWMLRAMNK 156
Cdd:COG0783    81 AEFAKLSTIKEEPeGVVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHLE 155
 
Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 3-156 7.66e-73

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: 215.08  E-value: 7.66e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1909714243   3 TINIGIPEADRVKIAESLKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSLDVFAPGTY 82
Cdd:COG0783     1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1909714243  83 KEFSKLSSVQEVD-GIPTSKEMVDILTKGHETIVQSCRDVLKFSQPADDESTIALASDRMRVHEKTAWMLRAMNK 156
Cdd:COG0783    81 AEFAKLSTIKEEPeGVVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHLE 155
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 18-154 5.05e-63

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: 189.68  E-value: 5.05e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1909714243  18 ESLKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSLDVFAPGTYKEFSKLSSVQEVD-G 96
Cdd:cd01043     1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPaG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1909714243  97 IPTSKEMVDILTKGHETIVQSCRDVLKFSQPADDESTIALASDRMRVHEKTAWMLRAM 154
Cdd:cd01043    81 VLSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAH 138
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 20-154 1.68e-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: 91.96  E-value: 1.68e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1909714243  20 LKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSLDVFAPGTYKEFSKLSSVQEVDGIPt 99
Cdd:pfam00210   4 LNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGTRVELLAIEAPPSFGSVL- 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1909714243 100 skEMVDILTKGHETIVQSCRDVLKFSQPADDESTIALASDRMRVHEKTAWMLRAM 154
Cdd:pfam00210  83 --EVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEAL 135
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
10-74 7.24e-17

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 73.06  E-value: 7.24e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1909714243  10 EADRVK-IAESLKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSL 74
Cdd:NF041388   17 DAEKAEqIVDALNTDLAATYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQAL 82
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 6-93 1.02e-13

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 64.62  E-value: 1.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1909714243   6 IGIPEADRVKIAESLKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSLDVFAPGTYKEF 85
Cdd:PRK09448   13 NDVPDSEKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVALGTTQVV 92


                  ....*...
gi 1909714243  86 SKLSSVQE 93
Cdd:PRK09448   93 ASKTPLKS 100
 
Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 3-156 7.66e-73

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: 215.08  E-value: 7.66e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1909714243   3 TINIGIPEADRVKIAESLKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSLDVFAPGTY 82
Cdd:COG0783     1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1909714243  83 KEFSKLSSVQEVD-GIPTSKEMVDILTKGHETIVQSCRDVLKFSQPADDESTIALASDRMRVHEKTAWMLRAMNK 156
Cdd:COG0783    81 AEFAKLSTIKEEPeGVVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHLE 155
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 18-154 5.05e-63

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: 189.68  E-value: 5.05e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1909714243  18 ESLKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSLDVFAPGTYKEFSKLSSVQEVD-G 96
Cdd:cd01043     1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPaG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1909714243  97 IPTSKEMVDILTKGHETIVQSCRDVLKFSQPADDESTIALASDRMRVHEKTAWMLRAM 154
Cdd:cd01043    81 VLSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAH 138
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 20-154 1.68e-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: 91.96  E-value: 1.68e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1909714243  20 LKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSLDVFAPGTYKEFSKLSSVQEVDGIPt 99
Cdd:pfam00210   4 LNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGTRVELLAIEAPPSFGSVL- 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1909714243 100 skEMVDILTKGHETIVQSCRDVLKFSQPADDESTIALASDRMRVHEKTAWMLRAM 154
Cdd:pfam00210  83 --EVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEAL 135
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
10-74 7.24e-17

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 73.06  E-value: 7.24e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1909714243  10 EADRVK-IAESLKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSL 74
Cdd:NF041388   17 DAEKAEqIVDALNTDLAATYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQAL 82
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 6-93 1.02e-13

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 64.62  E-value: 1.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1909714243   6 IGIPEADRVKIAESLKKLLADTYTLYLQTHNFHWNVTGPQFRDLHLMFEEQYNELALAVDDIAERIRSLDVFAPGTYKEF 85
Cdd:PRK09448   13 NDVPDSEKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVALGTTQVV 92


                  ....*...
gi 1909714243  86 SKLSSVQE 93
Cdd:PRK09448   93 ASKTPLKS 100
 
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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