1JI4,1N1Q,1JIG,1QGH,1O9R,1DPS


Conserved Protein Domain Family
DPS

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cd01043: DPS 
Click on image for an interactive view with Cn3D
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.
Statistics
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PSSM-Id: 153102
View PSSM: cd01043
Aligned: 201 rows
Threshold Bit Score: 98.0009
Threshold Setting Gi: 116333339
Created: 24-Sep-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DPS ferroxidaseion poredimerization
Conserved site includes 5 residues -Click on image for an interactive view with Cn3D
Feature 1:DPS ferroxidase diiron center [ion binding site]
Evidence:
  • Comment:DPS ferroxidase site is shared by 2-fold symmetry-related subunits providing the iron ligands.
  • Comment:putative site of iron oxidation
  • Structure:1N1Q; Bacillus brevis DPS dinuclear ferroxidase centers.
    View structure with Cn3D
  • Comment:DPS has two diiron binding sites at the dimer interface.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                           #           #   #          #   #                            
1JI4_A        5 EILKHLQADAIVLFMKVHNFHWNVKGTDFFNVHKATEEIYEEFADMFDDLAERIVQLGHHPLvTLSEAIKLTRVKEetk- 83  Helicobacter pylori
1N1Q_A       11 VLLNRQVANWVVLYVKLHNFHWNVNGPNFFTLHEKFEELYTEASGHIDTLAERVLSIGGSPIaTLAASLEEASIKEat-- 88  Brevibacillus br...
NP_692554     8 NFLNQLLSNYFVLYVKLHRYHWFVKGVHFFTLHDKFEEMYEQITVQLDEIAERILMIGGKPLaTMAKYIKESTIEEaa-- 85  Oceanobacillus i...
ZP_02184404  31 AMTNHIISNQAILHVKLHQYHWYVKGPNFFSLHEKFENLYDENAKYYDDIAERLIASGAKPAsTTEEYAKYGLISEsskd 110 Carnobacterium s...
ZP_04859546  10 YQMNKFLANLHIFKTIVHNYHWNLKGEHFFTIHPMLDGVMSETDEHIDEVAERILMIGGRPFaSLKVYLEHSMLQEies- 88  Fusobacterium va...
ZP_04564279   3 KQLNKLLADLVVEYHKLQSYHWYIKGKDFFTVHAKLEELYNGVNKAIDEVAEAILMTGFKPAaSMQEFLDISAIEEvkg- 81  Mollicutes bacte...
NP_786659    28 AMTNHILSNLMVAYVKLTQVKWYVKGPQSLALRTAYQRLLDQNVRQFAELGELLLDENQKPSsTTAELTKYSMLEEngaf 107 Lactobacillus pl...
YP_803948    27 AMTNHILANLRMMSTKLNQLEWYIKGNNYFADQQFLSSMRQTVDNYFNQLGHQLVNAGEKPSsITEEFSEYKMLTEnarn 106 Pediococcus pent...
YP_794866    27 AMTNHILANLHISIVKFHQVRWSVKGPLALSVRQLLTTYITTYRNQFDALGELLLDEGEIVStTTKEYHDYNMLQEggdk 106 Lactobacillus br...
ZP_04433176   8 RFLNQELSNFTVLYIKLHRYHWYIQGKNFFTLHAYFEDLYRSFSKQMDVLAERILAIGGRPLaTMSKFLDQKTLVEas-- 85  Bacillus coagula...
Feature 1                                                                    
1JI4_A       84 tsFHSKDIFKEILEDYKYLEKEFKELSNtae-kegDKVTVTYADDQLAKLQKSIWMLQAHL 143 Helicobacter pylori
1N1Q_A       89 ggESAAEMVSSVVNDFVDLVGELKVARDvad-eadDEATADMLDAIEAGLEKHVWMLEAFL 148 Brevibacillus brevis
NP_692554    86 adDEEAEIIQQLVKNITQLISEIQEEGYalteefhDHPTEDLLTSLHADLDKKKWMLESYQ 146 Oceanobacillus iheyensis HTE831
ZP_02184404 111 kyLSAEEMVGNLVDDYRLTRDLTLRTIRlaq-keeDFVLEDTMIGYKNYLDKTIWLLQAFL 170 Carnobacterium sp. AT7
ZP_04859546  89 kpYTGIEAVKGILENFKLLLDEMNVALKmae-dieDQETADLFTGIGAAYQKHIWMYTAWL 148 Fusobacterium varium ATCC 27725
ZP_04564279  82 ehITSKDIYKVVLNDFNYLLDRIKSLKNnad-nenNYLISSLMDDYIKEFTKSIWMISQVV 141 Mollicutes bacterium D7
NP_786659   108 kyQSVDELVAATIKDFDTENLFVDRAIKlae-kenRPALAAWLVAYRGSNNRNIRELQAYL 167 Lactobacillus plantarum WCFS1
YP_803948   107 kyLTDQEMLAMLVDDIQTSKMFISRAIIlaq-nesKFPLQNFLIELDGSFNQFSAAIQARL 166 Pediococcus pentosaceus ATCC 25745
YP_794866   107 kyYAATDQLNELIHDADTHNLFIDRAIKlae-kesRPALATFLVTLRGTNNHIIRELQAVL 166 Lactobacillus brevis ATCC 367
ZP_04433176  86 adNEEGELLQQLREDLAQLAKEIRETGIplaeenkDNATVNLLTRFLTRFDKDIWMLDAMA 146 Bacillus coagulans 36D1

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