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(-) Description

Title :  X-RAY STRUCTURE OF DPSA FROM THERMOSYNECHOCOCCUS ELONGATUS
 
Authors :  S. Franceschini, A. Ilari
Date :  14 Jul 08  (Deposition) - 17 Nov 09  (Release) - 23 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Stress Response Protein, Dna-Binding Protein, Dps, Oxidation, Iron Binding, Ferroxidase Centre (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Alaleona, S. Franceschini, P. Ceci, A. Ilari, E. Chiancone
Thermosynechococcus Elongatus Dpsa Binds Zn(Ii) At A Unique Three Histidine-Containing Ferroxidase Center And Utilizes O2 As Iron Oxidant With Very High Efficiency, Unlike The Typical Dps Proteins.
Febs J. V. 277 903 2010
PubMed-ID: 20088882  |  Reference-DOI: 10.1111/J.1742-4658.2009.07532.X

(-) Compounds

Molecule 1 - STARVATION INDUCED DNA BINDING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
    Organism Taxid: 32046
    Other Details: HIS-TAG AT C-TERMINAL

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4ZN8Ligand/IonZINC ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2PEG9Ligand/IonDI(HYDROXYETHYL)ETHER
3PG43Ligand/IonTETRAETHYLENE GLYCOL
4ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:51 , HIS B:78 , GLU B:82 , HOH B:2055 , HOH B:2057BINDING SITE FOR RESIDUE ZN A 201
02AC2SOFTWAREHIS A:63 , GLU B:82 , HOH B:2057 , HIS C:164BINDING SITE FOR RESIDUE ZN A 202
03AC3SOFTWAREGLU A:82 , HIS B:63 , HIS B:164 , HOH B:2050BINDING SITE FOR RESIDUE ZN B 201
04AC4SOFTWAREHIS A:78 , GLU A:82 , HIS B:51 , HOH B:2041BINDING SITE FOR RESIDUE ZN B 202
05AC5SOFTWAREGLU D:140BINDING SITE FOR RESIDUE FE B 203
06AC6SOFTWAREHIS C:63 , PEG C:1177 , HOH C:2106 , GLU D:82 , HIS D:164 , HOH D:2055BINDING SITE FOR RESIDUE ZN C 201
07AC7SOFTWAREHIS C:51 , HOH C:2046 , HIS D:78 , GLU D:82 , HOH D:2055BINDING SITE FOR RESIDUE ZN C 202
08AC8SOFTWAREGLU A:140 , GLU B:140 , GLU C:140BINDING SITE FOR RESIDUE FE C 203
09AC9SOFTWAREHIS A:164 , HOH A:2100 , GLU C:82 , HIS D:63 , ZN D:202 , HOH D:2037BINDING SITE FOR RESIDUE ZN D 201
10BC1SOFTWAREHIS C:78 , GLU C:82 , HIS D:51 , ZN D:201 , HOH D:2037BINDING SITE FOR RESIDUE ZN D 202
11BC2SOFTWAREALA A:99 , GLN B:96 , ALA B:99 , HOH B:2067 , ARG D:35 , ALA D:100 , HOH D:2030 , HOH D:2114BINDING SITE FOR RESIDUE PEG D1177
12BC3SOFTWAREPHE B:65 , ASP B:68 , GLN B:72 , LYS B:157 , GLU B:160 , ARG B:161 , HIS B:164 , HOH B:2121BINDING SITE FOR RESIDUE PG4 B1177
13BC4SOFTWARETHR B:105 , HOH B:2072BINDING SITE FOR RESIDUE PEG B1178
14BC5SOFTWAREGLN C:64 , GLN C:67 , ASP C:68 , ZN C:201 , HOH C:2106BINDING SITE FOR RESIDUE PEG C1177

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VXX)

(-) Exons   (0, 0)

(no "Exon" information available for 2VXX)

(-) 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:172
 aligned with Q8DL82_THEEB | Q8DL82 from UniProtKB/TrEMBL  Length:176

    Alignment length:172
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  
         Q8DL82_THEEB     5 ALPRQAFGEMADTVILLEKATTTPICEGMNRLLASFQALYLQYQKHHFVVEGAEFYPLHQFFQDCYEQVQDHVHALGERLNGLGGVPVAGFQQLAALCCFTPEPEGAFNCRQMLSNDLQAEQAIIGVLRQQATQAESLGDRATAYLYDQILLKTEERAYHIGHFLANDSLKV 176
               SCOP domains d2vxxa_ A: automated matches                                                                                                                                                 SCOP domains
               CATH domains 2vxxA00 A:5-176  [code=1.20.1260.10, no name defined]                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhh..........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxx A   5 ALPRQAFGEMADTVILLEKATTTPICEGMNRLLASFQALYLQYQKHHFVVEGAEFYPLHQFFQDCYEQVQDHVHALGERLNGLGGVPVAGFQQLAALCCFTPEPEGAFNCRQMLSNDLQAEQAIIGVLRQQATQAESLGDRATAYLYDQILLKTEERAYHIGHFLANDSLKV 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q8DL82_THEEB | Q8DL82 from UniProtKB/TrEMBL  Length:176

    Alignment length:173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   
         Q8DL82_THEEB     4 SALPRQAFGEMADTVILLEKATTTPICEGMNRLLASFQALYLQYQKHHFVVEGAEFYPLHQFFQDCYEQVQDHVHALGERLNGLGGVPVAGFQQLAALCCFTPEPEGAFNCRQMLSNDLQAEQAIIGVLRQQATQAESLGDRATAYLYDQILLKTEERAYHIGHFLANDSLKV 176
               SCOP domains d2vxxb_ B: automated matches                                                                                                                                                  SCOP domains
               CATH domains 2vxxB00 B:4-176  [code=1.20.1260.10, no name defined]                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhh..........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxx B   4 SALPRQAFGEMADTVILLEKATTTPICEGMNRLLASFQALYLQYQKHHFVVEGAEFYPLHQFFQDCYEQVQDHVHALGERLNGLGGVPVAGFQQLAALCCFTPEPEGAFNCRQMLSNDLQAEQAIIGVLRQQATQAESLGDRATAYLYDQILLKTEERAYHIGHFLANDSLKV 176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   


Chain C from PDB  Type:PROTEIN  Length:173
 aligned with Q8DL82_THEEB | Q8DL82 from UniProtKB/TrEMBL  Length:176

    Alignment length:173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   
         Q8DL82_THEEB     4 SALPRQAFGEMADTVILLEKATTTPICEGMNRLLASFQALYLQYQKHHFVVEGAEFYPLHQFFQDCYEQVQDHVHALGERLNGLGGVPVAGFQQLAALCCFTPEPEGAFNCRQMLSNDLQAEQAIIGVLRQQATQAESLGDRATAYLYDQILLKTEERAYHIGHFLANDSLKV 176
               SCOP domains d2vxxc_ C: automated matches                                                                                                                                                  SCOP domains
               CATH domains 2vxxC00 C:4-176  [code=1.20.1260.10, no name defined]                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhh..........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxx C   4 SALPRQAFGEMADTVILLEKATTTPICEGMNRLLASFQALYLQYQKHHFVVEGAEFYPLHQFFQDCYEQVQDHVHALGERLNGLGGVPVAGFQQLAALCCFTPEPEGAFNCRQMLSNDLQAEQAIIGVLRQQATQAESLGDRATAYLYDQILLKTEERAYHIGHFLANDSLKV 176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   


Chain D from PDB  Type:PROTEIN  Length:172
 aligned with Q8DL82_THEEB | Q8DL82 from UniProtKB/TrEMBL  Length:176

    Alignment length:172
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  
         Q8DL82_THEEB     5 ALPRQAFGEMADTVILLEKATTTPICEGMNRLLASFQALYLQYQKHHFVVEGAEFYPLHQFFQDCYEQVQDHVHALGERLNGLGGVPVAGFQQLAALCCFTPEPEGAFNCRQMLSNDLQAEQAIIGVLRQQATQAESLGDRATAYLYDQILLKTEERAYHIGHFLANDSLKV 176
               SCOP domains d2vxxd_ D: automated matches                                                                                                                                                 SCOP domains
               CATH domains 2vxxD00 D:5-176  [code=1.20.1260.10, no name defined]                                                                                                                        CATH domains
           Pfam domains (1) -------------------------Ferritin-2vxxD01 D:30-174                                                                                                                        -- Pfam domains (1)
           Pfam domains (2) -------------------------Ferritin-2vxxD02 D:30-174                                                                                                                        -- Pfam domains (2)
           Pfam domains (3) -------------------------Ferritin-2vxxD03 D:30-174                                                                                                                        -- Pfam domains (3)
           Pfam domains (4) -------------------------Ferritin-2vxxD04 D:30-174                                                                                                                        -- Pfam domains (4)
         Sec.struct. author .................hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhh..........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxx D   5 ALPRQAFGEMADTVILLEKATTTPICEGMNRLLASFQALYLQYQKHHFVVEGAEFYPLHQFFQDCYEQVQDHVHALGERLNGLGGVPVAGFQQLAALCCFTPEPEGAFNCRQMLSNDLQAEQAIIGVLRQQATQAESLGDRATAYLYDQILLKTEERAYHIGHFLANDSLKV 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8DL82_THEEB | Q8DL82)
molecular function
    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: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:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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