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Conserved domains on  [gi|445993010|ref|WP_000070865|]
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MULTISPECIES: Dps family protein [Staphylococcus]

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; belongs to the ferritin-like superfamily of diiron-containing four-helix-bundle proteins

CATH:  1.20.1260.10
EC:  1.16.-.-
Gene Ontology:  GO:0016722|GO:0008199
PubMed:  12767829|8749363|9444766|9546221|12730463
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 ...
 1-146 2.71e-62

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: 188.12  E-value: 2.71e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010   1 MSNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQS 80
Cdd:COG0783    8 EEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTLAEFAKLS 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 445993010  81 IVKEAAKG-YSAEQMVEELSQDFTNISKQLEKAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYL 146
Cdd:COG0783   88 TIKEEPEGvVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHL 154
 
Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 1-146 2.71e-62

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: 188.12  E-value: 2.71e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010   1 MSNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQS 80
Cdd:COG0783    8 EEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTLAEFAKLS 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 445993010  81 IVKEAAKG-YSAEQMVEELSQDFTNISKQLEKAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYL 146
Cdd:COG0783   88 TIKEEPEGvVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHL 154
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 9-146 6.93e-62

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: 186.60  E-value: 6.93e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010   9 KELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKEAAKG 88
Cdd:cd01043    1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPAG 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 445993010  89 Y-SAEQMVEELSQDFTNISKQLEKAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYL 146
Cdd:cd01043   81 VlSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAHL 139
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 8-146 2.83e-29

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: 103.91  E-value: 2.83e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010    8 VKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEqsiVKEAAK 87
Cdd:pfam00210   1 IAALNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGTRVELLA---IEAPPS 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 445993010   88 GYSAEQMVEELSQDFTNISKQLEKAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYL 146
Cdd:pfam00210  78 FGSVLEVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEALL 136
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 5-146 3.22e-19

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 78.49  E-value: 3.22e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010   5 QDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKE 84
Cdd:PRK09448  21 KATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVALGTTQVVASKTPLKS 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 445993010  85 AAKG-YSAEQMVEELSQDFTNISKQLEKAIeiaGNAGDDVSEDMFIGMQTSVDKHNWMFKSYL 146
Cdd:PRK09448 101 YPLDiHNVQDHLKALADRYAIVANDVRKAI---DEAGDEDTADIFTAASRDLDKFLWFIEAHI 160
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
7-127 2.91e-17

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 73.83  E-value: 2.91e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010   7 VVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVK-EA 85
Cdd:NF041388  24 IVDALNTDLAATYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQALGGVPVSGPAALEEHAPVEpEG 103

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 445993010  86 AKGYSAEQMVEELSQDFTNISKQLEKAIEIAGNAGDDVSEDM 127
Cdd:NF041388 104 EDVYDIRTSLENDLEMYGDIIESVRDHIELAENLGDHATAEL 145
 
Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 1-146 2.71e-62

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: 188.12  E-value: 2.71e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010   1 MSNQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQS 80
Cdd:COG0783    8 EEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTLAEFAKLS 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 445993010  81 IVKEAAKG-YSAEQMVEELSQDFTNISKQLEKAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYL 146
Cdd:COG0783   88 TIKEEPEGvVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHL 154
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 9-146 6.93e-62

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: 186.60  E-value: 6.93e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010   9 KELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKEAAKG 88
Cdd:cd01043    1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPAG 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 445993010  89 Y-SAEQMVEELSQDFTNISKQLEKAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYL 146
Cdd:cd01043   81 VlSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAHL 139
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 8-146 2.83e-29

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: 103.91  E-value: 2.83e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010    8 VKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEqsiVKEAAK 87
Cdd:pfam00210   1 IAALNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGTRVELLA---IEAPPS 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 445993010   88 GYSAEQMVEELSQDFTNISKQLEKAIEIAGNAGDDVSEDMFIGMQTSVDKHNWMFKSYL 146
Cdd:pfam00210  78 FGSVLEVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEALL 136
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 5-146 3.22e-19

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 78.49  E-value: 3.22e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010   5 QDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVKE 84
Cdd:PRK09448  21 KATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVALGTTQVVASKTPLKS 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 445993010  85 AAKG-YSAEQMVEELSQDFTNISKQLEKAIeiaGNAGDDVSEDMFIGMQTSVDKHNWMFKSYL 146
Cdd:PRK09448 101 YPLDiHNVQDHLKALADRYAIVANDVRKAI---DEAGDEDTADIFTAASRDLDKFLWFIEAHI 160
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
7-127 2.91e-17

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 73.83  E-value: 2.91e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010   7 VVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPVGTLTECLEQSIVK-EA 85
Cdd:NF041388  24 IVDALNTDLAATYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQALGGVPVSGPAALEEHAPVEpEG 103

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 445993010  86 AKGYSAEQMVEELSQDFTNISKQLEKAIEIAGNAGDDVSEDM 127
Cdd:NF041388 104 EDVYDIRTSLENDLEMYGDIIESVRDHIELAENLGDHATAEL 145
Bfr COG2193
Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism];
5-141 1.48e-06

Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism];


Pssm-ID: 441796  Cd Length: 152  Bit Score: 44.80  E-value: 1.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445993010   5 QDVVKELNQQVANWTVA---YTkLHNFHwyVKGPNFFSLHVKFEELYNEASQYVDELAERILAVGGNPvgtlteclEQSI 81
Cdd:COG2193    3 PKVIELLNKALANELTAinqYF-LHARM--LKNWGLEKLAEKFYEESIEEMKHADKLIERILFLGGLP--------NLQD 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 445993010  82 VKEAAKGYSAEQMVE---ELSQDftnISKQLEKAIEIAGNAGDDVSEDMFIGMQTSVDKH-NWM 141
Cdd:COG2193   72 LGKLRIGEDVEEMLEcdlALELE---AIALYREAIALCEEVGDYVSRDLLEEILEDEEEHiDWL 132
 
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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