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(-) Description

Title :  DPS FROM DEINOCOCCUS RADIODURANS
 
Authors :  C. V. Romao, E. Mitchell, S. Mcsweeney
Date :  30 Sep 05  (Deposition) - 26 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Dna-Binding Protein, Dps, Iron, Deinococcus Radiodurans, Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. V. Romao, E. Mitchell, S. Mcsweeney
The Crystal Structure Of Deinococcus Radiodurans Dps Protein (Dr2263) Reveals The Presence Of A Novel Metal Centre In The N Terminus.
J. Biol. Inorg. Chem. V. 11 891 2006
PubMed-ID: 16855817  |  Reference-DOI: 10.1007/S00775-006-0142-5

(-) Compounds

Molecule 1 - DNA-BINDING STRESS RESPONSE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: R1
    Synonym: DPS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2SO41Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2SO412Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:89 , ARG A:205BINDING SITE FOR RESIDUE SO4 A1208
2AC2SOFTWAREASP A:36 , HIS A:39 , HIS A:50 , GLU A:55BINDING SITE FOR RESIDUE ZN A1209
3AC3SOFTWAREASP A:93 , HOH A:2154BINDING SITE FOR RESIDUE FE A1210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C2U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C2U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C2U)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DPS_1PS00818 Dps protein family signature 1.DPS1_DEIRA83-99  1A:83-99
Biological Unit 1 (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DPS_1PS00818 Dps protein family signature 1.DPS1_DEIRA83-99  12A:83-99

(-) Exons   (0, 0)

(no "Exon" information available for 2C2U)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:178
 aligned with DPS1_DEIRA | Q9RS64 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:178
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199        
           DPS1_DEIRA    30 GGADHADAAHLGTVNNALVNHHYLEEKEFQTVAETLQRNLATTISLYLKFKKYHWDIRGRFFRDLHLAYDEFIAEIFPSIDEQAERLVALGGSPLAAPADLARYSTVQVPQETVRDARTQVADLVQDLSRVGKGYRDDSQACDEANDPVTADMYNGYAATIDKIRWMLQAIMDDERLD 207
               SCOP domains d2c2ua_ A: automated matches                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------DPS_1            ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c2u A  30 GGADHADAAHLGTVNNALVNHHYLEEKEFQTVAETLQRNLATTISLYLKFKKYHWDIRGRFFRDLHLAYDEFIAEIFPSIDEQAERLVALGGSPLAAPADLARYSTVQVPQETVRDARTQVADLVQDLSRVGKGYRDDSQACDEANDPVTADMYNGYAATIDKIRWMLQAIMDDERLD 207
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C2U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C2U)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (DPS1_DEIRA | Q9RS64)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016722    oxidoreductase activity, oxidizing metal ions    Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009295    nucleoid    The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DPS1_DEIRA | Q9RS64: 2c2f 2f7n

(-) Related Entries Specified in the PDB File

2c2f DPS FROM DEINOCOCCUS RADIODURANS