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Conserved domains on  [gi|1437098156|emb|SUM43326|]
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Non-specific DNA-binding protein Dps / Iron-binding ferritin-like antioxidant protein / Ferroxidase [Staphylococcus petrasii]

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 ...
 1-145 1.50e-60

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: 183.88  E-value: 1.50e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   1 MAQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSI 80
Cdd:COG0783     9 EAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTLAEFAKLST 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1437098156  81 VEEAGKG-YKAEEMVEEFSKDLTNISKQLETAIKVAGDAGDDVSEDMFIGMQTSVDKHNWMLKSYL 145
Cdd:COG0783    89 IKEEPEGvVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHL 154
 
Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 1-145 1.50e-60

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: 183.88  E-value: 1.50e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   1 MAQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSI 80
Cdd:COG0783     9 EAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTLAEFAKLST 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1437098156  81 VEEAGKG-YKAEEMVEEFSKDLTNISKQLETAIKVAGDAGDDVSEDMFIGMQTSVDKHNWMLKSYL 145
Cdd:COG0783    89 IKEEPEGvVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHL 154
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 8-145 3.67e-60

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: 181.97  E-value: 3.67e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   8 KELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSIVEEAGKG 87
Cdd:cd01043     1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPAG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1437098156  88 Y-KAEEMVEEFSKDLTNISKQLETAIKVAGDAGDDVSEDMFIGMQTSVDKHNWMLKSYL 145
Cdd:cd01043    81 VlSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAHL 139
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 7-145 5.60e-30

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: 105.45  E-value: 5.60e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   7 VKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSIVEEAGk 86
Cdd:pfam00210   1 IAALNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGTRVELLAIEAPPSFG- 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1437098156  87 gyKAEEMVEEFSKDLTNISKQLETAIKVAGDAGDDVSEDMFIGMQTSVDKHNWMLKSYL 145
Cdd:pfam00210  80 --SVLEVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEALL 136
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 2-145 6.59e-17

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 72.71  E-value: 6.59e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   2 AQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSIV 81
Cdd:PRK09448   19 EKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVALGTTQVVASKTPL 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1437098156  82 EEAGKG-YKAEEMVEEFSKDLTNISKQLETAIkvaGDAGDDVSEDMFIGMQTSVDKHNWMLKSYL 145
Cdd:PRK09448   99 KSYPLDiHNVQDHLKALADRYAIVANDVRKAI---DEAGDEDTADIFTAASRDLDKFLWFIEAHI 160
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
2-126 4.01e-14

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 65.36  E-value: 4.01e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   2 AQQdVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSIV 81
Cdd:NF041388   21 AEQ-IVDALNTDLAATYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQALGGVPVSGPAALEEHAPV 99

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1437098156  82 EEAGKG-YKAEEMVEEfskDLT---NISKQLETAIKVAGDAGDDVSEDM 126
Cdd:NF041388  100 EPEGEDvYDIRTSLEN---DLEmygDIIESVRDHIELAENLGDHATAEL 145
 
Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 1-145 1.50e-60

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: 183.88  E-value: 1.50e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   1 MAQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSI 80
Cdd:COG0783     9 EAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTLAEFAKLST 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1437098156  81 VEEAGKG-YKAEEMVEEFSKDLTNISKQLETAIKVAGDAGDDVSEDMFIGMQTSVDKHNWMLKSYL 145
Cdd:COG0783    89 IKEEPEGvVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHL 154
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 8-145 3.67e-60

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: 181.97  E-value: 3.67e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   8 KELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSIVEEAGKG 87
Cdd:cd01043     1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPAG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1437098156  88 Y-KAEEMVEEFSKDLTNISKQLETAIKVAGDAGDDVSEDMFIGMQTSVDKHNWMLKSYL 145
Cdd:cd01043    81 VlSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAHL 139
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 7-145 5.60e-30

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: 105.45  E-value: 5.60e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   7 VKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSIVEEAGk 86
Cdd:pfam00210   1 IAALNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGTRVELLAIEAPPSFG- 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1437098156  87 gyKAEEMVEEFSKDLTNISKQLETAIKVAGDAGDDVSEDMFIGMQTSVDKHNWMLKSYL 145
Cdd:pfam00210  80 --SVLEVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEALL 136
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 2-145 6.59e-17

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 72.71  E-value: 6.59e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   2 AQQDVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSIV 81
Cdd:PRK09448   19 EKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVALGTTQVVASKTPL 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1437098156  82 EEAGKG-YKAEEMVEEFSKDLTNISKQLETAIkvaGDAGDDVSEDMFIGMQTSVDKHNWMLKSYL 145
Cdd:PRK09448   99 KSYPLDiHNVQDHLKALADRYAIVANDVRKAI---DEAGDEDTADIFTAASRDLDKFLWFIEAHI 160
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
2-126 4.01e-14

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 65.36  E-value: 4.01e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   2 AQQdVVKELNQQVANWTVAYTKLHNFHWYVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPVGTLKESLDLSIV 81
Cdd:NF041388   21 AEQ-IVDALNTDLAATYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQALGGVPVSGPAALEEHAPV 99

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1437098156  82 EEAGKG-YKAEEMVEEfskDLT---NISKQLETAIKVAGDAGDDVSEDM 126
Cdd:NF041388  100 EPEGEDvYDIRTSLEN---DLEmygDIIESVRDHIELAENLGDHATAEL 145
Bfr COG2193
Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism];
4-140 2.65e-09

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


Pssm-ID: 441796  Cd Length: 152  Bit Score: 52.50  E-value: 2.65e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156   4 QDVVKELNQQVANWTVA---YTkLHNFHwyVKGPNFFSLHAKFEELYNEASQYVDDLAERILAIGGNPvgtlkeslDLSI 80
Cdd:COG2193     3 PKVIELLNKALANELTAinqYF-LHARM--LKNWGLEKLAEKFYEESIEEMKHADKLIERILFLGGLP--------NLQD 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1437098156  81 VEEAGKGYKAEEMVEEfskDL---TNISKQLETAIKVAGDAGDDVSEDMFIGMQTSVDKH-NWM 140
Cdd:COG2193    72 LGKLRIGEDVEEMLEC---DLaleLEAIALYREAIALCEEVGDYVSRDLLEEILEDEEEHiDWL 132
Bacterioferritin cd00907
Bacterioferritin, ferritin-like diiron-binding domain; Bacterioferritins, also known as ...
 39-127 6.51e-03

Bacterioferritin, ferritin-like diiron-binding domain; Bacterioferritins, also known as cytochrome b1, are members of a broad superfamily of ferritin-like diiron-carboxylate proteins. Similar to ferritin in architecture, Bfr forms an oligomer of 24 subunits that assembles to form a hollow sphere with 432 symmetry. Up to 12 heme cofactor groups (iron protoporphyrin IX or coproporphyrin III) are bound between dimer pairs. The role of the heme is unknown, although it may be involved in mediating iron-core reduction and iron release. Each subunit is composed of a four-helix bundle which carries a diiron ferroxidase center; it is here that initial oxidation of ferrous iron by molecular oxygen occurs, facilitating the detoxification of iron, protection against dioxygen and radical products, and storage of ferric-hydroxyphosphate at the core. Some bacterioferritins are composed of two subunit types, one conferring heme-binding ability (alpha) and the other (beta) bestowing ferroxidase activity.


Pssm-ID: 153099  Cd Length: 153  Bit Score: 34.83  E-value: 6.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1437098156  39 LHAK------FEELYN-------EASQYVDDLAERILAIGGNPvgtlkesldlsIVEEAGKGYKAEEMVEEFSKDLT--- 102
Cdd:cd00907    26 LHARmledwgLEKLAErfrkesiEEMKHADKLIERILFLEGLP-----------NLQRLGKLRIGEDVPEMLENDLAley 94

                          90       100
                  ....*....|....*....|....*
gi 1437098156 103 NISKQLETAIKVAGDAGDDVSEDMF 127
Cdd:cd00907    95 EAIAALNEAIALCEEVGDYVSRDLL 119
 
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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