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Conserved domains on  [gi|640673685|ref|WP_025098510|]
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MULTISPECIES: Dps family protein [Burkholderia]

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 ...
 9-162 6.84e-81

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: 235.88  E-value: 6.84e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685   9 QINIGISDKDRKKIAEGLSKLLADTFSLYLKTHYFHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLGVVAPGTY 88
Cdd:COG0783    1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 640673685  89 GDFAKLTVVPE-ASGVPAAEEMIRQLVEGHEAVVRTARGIFPDADSVGDEPTADLLTQRLQTHEKTAWMLRSLLQ 162
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 ...
 9-162 6.84e-81

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: 235.88  E-value: 6.84e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685   9 QINIGISDKDRKKIAEGLSKLLADTFSLYLKTHYFHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLGVVAPGTY 88
Cdd:COG0783    1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 640673685  89 GDFAKLTVVPE-ASGVPAAEEMIRQLVEGHEAVVRTARGIFPDADSVGDEPTADLLTQRLQTHEKTAWMLRSLLQ 162
Cdd:COG0783   81 AEFAKLSTIKEePEGVVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHLE 155
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 24-161 4.55e-64

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: 192.76  E-value: 4.55e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685  24 EGLSKLLADTFSLYLKTHYFHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLGVVAPGTYGDFAKLTVVPEAS-G 102
Cdd:cd01043    1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPaG 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 640673685 103 VPAAEEMIRQLVEGHEAVVRTARGIFPDADSVGDEPTADLLTQRLQTHEKTAWMLRSLL 161
Cdd:cd01043   81 VLSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAHL 139
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 23-162 6.24e-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: 106.22  E-value: 6.24e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685   23 AEGLSKLLADTFSLYLKTHYFHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLGVVAPGTYGDFAKLTVVPEASG 102
Cdd:pfam00210   1 IAALNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGTRVELLAIEAPPSFGS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685  103 VpaaEEMIRQLVEGHEAVVRTARGIFPDADSVGDEPTADLLTQRLQTHEKTAWMLRSLLQ 162
Cdd:pfam00210  81 V---LEVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEALLE 137
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 12-162 2.92e-21

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 84.27  E-value: 2.92e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685  12 IGISDKDRKKIAEGLSKLLADTFSLYLKTHYFHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLGVVAPGTYGDF 91
Cdd:PRK09448  13 NDVPDSEKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVALGTTQVV 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 640673685  92 AKLTVVPE-ASGVPAAEEMIRQLVEGHEAVVRTAR-GIfpdaDSVGDEPTADLLTQRLQTHEKTAWMLRSLLQ 162
Cdd:PRK09448  93 ASKTPLKSyPLDIHNVQDHLKALADRYAIVANDVRkAI----DEAGDEDTADIFTAASRDLDKFLWFIEAHIE 161
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
16-154 4.54e-17

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 73.83  E-value: 4.54e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685  16 DKDR-KKIAEGLSKLLADTFSLY--LKTHyfHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLG---VVAPGTYG 89
Cdd:NF041388  17 DAEKaEQIVDALNTDLAATYVLYhqLKKH--HWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQALGgvpVSGPAALE 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 640673685  90 DFAklTVVPEASGVPAAEEMIRQLVEGHEAVVRTARGIFPDADSVGDEPTADLLTQRLQTHEKTA 154
Cdd:NF041388  95 EHA--PVEPEGEDVYDIRTSLENDLEMYGDIIESVRDHIELAENLGDHATAELLREQLVELEEDA 157
 
Name Accession Description Interval E-value
Dps COG0783
DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and ...
 9-162 6.84e-81

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: 235.88  E-value: 6.84e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685   9 QINIGISDKDRKKIAEGLSKLLADTFSLYLKTHYFHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLGVVAPGTY 88
Cdd:COG0783    1 KTPIGLDEEAREKVAEALNQLLADLYVLYLKTKNAHWNVKGPNFFSLHELFEELYDELREAIDEIAERIRALGGVPPGTL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 640673685  89 GDFAKLTVVPE-ASGVPAAEEMIRQLVEGHEAVVRTARGIFPDADSVGDEPTADLLTQRLQTHEKTAWMLRSLLQ 162
Cdd:COG0783   81 AEFAKLSTIKEePEGVVDAREMVEALLEDYEALIKTLREAIELADEAGDEGTADLLTDILRELEKRAWMLRAHLE 155
DPS cd01043
DPS protein, ferritin-like diiron-binding domain; DPS (DNA Protecting protein under Starved ...
 24-161 4.55e-64

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: 192.76  E-value: 4.55e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685  24 EGLSKLLADTFSLYLKTHYFHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLGVVAPGTYGDFAKLTVVPEAS-G 102
Cdd:cd01043    1 EALNQLLADLYVLYLKLKNYHWNVKGPNFFALHELFEELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPaG 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 640673685 103 VPAAEEMIRQLVEGHEAVVRTARGIFPDADSVGDEPTADLLTQRLQTHEKTAWMLRSLL 161
Cdd:cd01043   81 VLSAKEMVAELLEDYETLIEELREAIELADEAGDPATADLLTEIIRELEKQAWMLRAHL 139
Ferritin pfam00210
Ferritin-like domain; This family contains ferritins and other ferritin-like proteins such as ...
 23-162 6.24e-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: 106.22  E-value: 6.24e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685   23 AEGLSKLLADTFSLYLKTHYFHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLGVVAPGTYGDFAKLTVVPEASG 102
Cdd:pfam00210   1 IAALNEQLADELTASYQYLQMHWYVKGPGFEGLHEFFDEQAEEEREHADKLAERILDLGGTPNGTRVELLAIEAPPSFGS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685  103 VpaaEEMIRQLVEGHEAVVRTARGIFPDADSVGDEPTADLLTQRLQTHEKTAWMLRSLLQ 162
Cdd:pfam00210  81 V---LEVLEAALEHEKKVTKSLRELIELAEEEGDYATADFLQWFLDEQEEHEWFLEALLE 137
PRK09448 PRK09448
DNA starvation/stationary phase protection protein Dps; Provisional
 12-162 2.92e-21

DNA starvation/stationary phase protection protein Dps; Provisional


Pssm-ID: 236521  Cd Length: 162  Bit Score: 84.27  E-value: 2.92e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685  12 IGISDKDRKKIAEGLSKLLADTFSLYLKTHYFHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLGVVAPGTYGDF 91
Cdd:PRK09448  13 NDVPDSEKKATIELLNQQLAQFIDLSLITKQAHWNMKGANFIAVHEMLDGFRTALEDHLDTMAERAVQLGGVALGTTQVV 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 640673685  92 AKLTVVPE-ASGVPAAEEMIRQLVEGHEAVVRTAR-GIfpdaDSVGDEPTADLLTQRLQTHEKTAWMLRSLLQ 162
Cdd:PRK09448  93 ASKTPLKSyPLDIHNVQDHLKALADRYAIVANDVRkAI----DEAGDEDTADIFTAASRDLDKFLWFIEAHIE 161
DNAstvprot_Halo NF041388
DNA starvation/stationary phase protection protein DpsA;
16-154 4.54e-17

DNA starvation/stationary phase protection protein DpsA;


Pssm-ID: 469279 [Multi-domain]  Cd Length: 171  Bit Score: 73.83  E-value: 4.54e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685  16 DKDR-KKIAEGLSKLLADTFSLY--LKTHyfHWNVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLG---VVAPGTYG 89
Cdd:NF041388  17 DAEKaEQIVDALNTDLAATYVLYhqLKKH--HWNVEGAEFRDLHLFLGEAAEDAEEAADELAERAQALGgvpVSGPAALE 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 640673685  90 DFAklTVVPEASGVPAAEEMIRQLVEGHEAVVRTARGIFPDADSVGDEPTADLLTQRLQTHEKTA 154
Cdd:NF041388  95 EHA--PVEPEGEDVYDIRTSLENDLEMYGDIIESVRDHIELAENLGDHATAELLREQLVELEEDA 157
DPSL cd01052
DPS-like protein, ferritin-like diiron-binding domain; DPSL (DPS-like). DPSL is a ...
 18-151 8.68e-05

DPS-like protein, ferritin-like diiron-binding domain; DPSL (DPS-like). DPSL is a phylogenetically distinct class within the ferritin-like superfamily, and similar in many ways to the DPS (DNA Protecting protein under Starved conditions) proteins. Like DPS, these proteins are expressed in response to oxidative stress, form dodecameric cage-like particles, preferentially utilize hydrogen peroxide in the controlled oxidation of iron, and possess a short N-terminal extension implicated in stabilizing cellular DNA. This domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. These proteins are distantly related to bacterial ferritins which assemble 24 monomers, each of which have a four-helix bundle with a fifth shorter helix at the C terminus and a diiron (ferroxidase) center. Ferritins contain a center where oxidation of ferrous iron by molecular oxygen occurs, facilitating the detoxification of iron, protection against dioxygen and radical products, and storage of iron in the ferric form. Many of the conserved residues of a diiron center are present in this domain.


Pssm-ID: 153111  Cd Length: 148  Bit Score: 40.35  E-value: 8.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640673685  18 DRKKIAEGLSKLLADTFSLYlkthYFHW----NVTGPMFNTLHLMFEEQYNELWLAVDSVAERIRTLGVVAPGTYGDFAK 93
Cdd:cd01052    3 DVDELIELLNKAFADEWLAY----YYYTilakHVKGPEGEGIKEELEEAAEEELNHAELLAERIYELGGTPPRDPKDWYE 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 640673685  94 LTVV---PEASGVPAAEEMIRQLVEGHEAVVRTARGIFpDADSVGDEPTADLLTQRLQ---THE 151
Cdd:cd01052   79 ISGCkcgYLPPDPPDVKGILKVNLKAERCAIKVYKELC-DMTHGKDPVTYDLALAILNeeiEHE 141
 
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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