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(-) Description

Title :  A DODECAMERIC THIOFERRITIN IN THE BACTERIAL DOMAIN, CHARACTERIZATION OF THE BACTERIOFERRITIN-RELATED PROTEIN FROM BACTEROIDES FRAGILIS
 
Authors :  G. H. Gauss, M. J. Young, T. Douglas, C. M. Lawrence
Date :  31 Jul 08  (Deposition) - 17 Nov 09  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Dps, Dpsl, Iron, Ferritin, Oxidative Stress, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. H. Gauss, M. A. Reott, E. R. Rocha, M. J. Young, T. Douglas, C. J. Smith C. M. Lawrence
Characterization Of The Bacteroides Fragilis Bfr Gene Product Identifies A Bacterial Dps-Like Protein And Suggests Evolutionary Links In The Ferritin Superfamily.
J. Bacteriol. V. 194 15 2012
PubMed-ID: 22020642  |  Reference-DOI: 10.1128/JB.05260-11

(-) Compounds

Molecule 1 - PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
    Atcc: 25285
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 272559
    Other Details: AMERICAN TYPE CULTURE COLLECTION (ATCC)
    Strain: NCTC 9343
    Synonym: BACTERIOFERRITIN-RELATED PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2FE8Ligand/IonFE (III) ION
3MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2FE-1Ligand/IonFE (III) ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:54 , HIS A:58 , ASP A:152 , HOH A:2033 , HOH A:2077 , HOH A:2081BINDING SITE FOR RESIDUE MG A 1001
02AC2SOFTWAREGLU A:29 , GLU A:62 , HIS A:65 , GLU A:146 , HOH A:2016BINDING SITE FOR RESIDUE FE A 6204
03AC3SOFTWAREGLU A:62 , GLU A:114 , GLU A:146 , HIS A:149 , HOH A:2061BINDING SITE FOR RESIDUE FE A 6205
04AC4SOFTWAREGLU B:54 , HIS B:58 , ASP B:152 , HOH B:2028 , HOH B:2071 , HOH B:2072BINDING SITE FOR RESIDUE MG B 1001
05AC5SOFTWAREGLU B:29 , GLU B:62 , HIS B:65 , GLU B:146 , HOH B:2033BINDING SITE FOR RESIDUE FE B 6204
06AC6SOFTWAREGLU B:62 , GLU B:114 , GLU B:146 , HIS B:149 , HOH B:2055BINDING SITE FOR RESIDUE FE B 6205
07AC7SOFTWAREGLU C:54 , HIS C:58 , ASP C:152 , HOH C:2028 , HOH C:2072 , HOH C:2074BINDING SITE FOR RESIDUE MG C 1001
08AC8SOFTWAREGLU C:29 , GLU C:62 , HIS C:65 , GLU C:146 , HOH C:2008BINDING SITE FOR RESIDUE FE C 6204
09AC9SOFTWAREGLU C:62 , GLU C:114 , GLU C:146 , HIS C:149 , HOH C:2033BINDING SITE FOR RESIDUE FE C 6205
10BC1SOFTWAREGLU D:54 , HIS D:58 , ASP D:152 , HOH D:2024 , HOH D:2083 , HOH D:2084BINDING SITE FOR RESIDUE MG D 1001
11BC2SOFTWAREGLU D:29 , GLU D:62 , HIS D:65 , GLU D:146 , HOH D:2029BINDING SITE FOR RESIDUE FE D 6204
12BC3SOFTWAREGLU D:62 , GLU D:114 , GLU D:146 , HIS D:149 , HOH D:2062BINDING SITE FOR RESIDUE FE D 6205
13BC4SOFTWAREGLN A:10 , GLY A:11 , LEU A:13 , ASP A:14BINDING SITE FOR RESIDUE BEN A 1170

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:93 -A:116
2B:93 -B:116
3C:93 -C:116
4D:93 -D:116

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VZB)

(-) 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:168
 aligned with Q5LAA6_BACFN | Q5LAA6 from UniProtKB/TrEMBL  Length:170

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
         Q5LAA6_BACFN     2 AKESVKILQGKLDVKSLIDQLNAALSEEWLAYYQYWVGALVVEGAMRADVQGEFEEHAEEERHHAQLIADRIIELEGVPVLDPKKWFELARCKYDSPTAFDSVSLLNQNVSSERCAILRYQEIANFTNGKDYTTCDIAKHILAEEEEHEQDLQDYLTDIARMKESFLK 169
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vzb A   2 AKESVKILQGKLDVKSLIDQLNAALSEEWLAYYQYWVGALVVEGAMRADVQGEFEEHAEEERHHAQLIADRIIELEGVPVLDPKKWFELARCKYDSPTAFDSVSLLNQNVSSERCAILRYQEIANFTNGKDYTTCDIAKHILAEEEEHEQDLQDYLTDIARMKESFLK 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with Q5LAA6_BACFN | Q5LAA6 from UniProtKB/TrEMBL  Length:170

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
         Q5LAA6_BACFN     2 AKESVKILQGKLDVKSLIDQLNAALSEEWLAYYQYWVGALVVEGAMRADVQGEFEEHAEEERHHAQLIADRIIELEGVPVLDPKKWFELARCKYDSPTAFDSVSLLNQNVSSERCAILRYQEIANFTNGKDYTTCDIAKHILAEEEEHEQDLQDYLTDIARMKESFL 168
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzb B   2 AKESVKILQGKLDVKSLIDQLNAALSEEWLAYYQYWVGALVVEGAMRADVQGEFEEHAEEERHHAQLIADRIIELEGVPVLDPKKWFELARCKYDSPTAFDSVSLLNQNVSSERCAILRYQEIANFTNGKDYTTCDIAKHILAEEEEHEQDLQDYLTDIARMKESFL 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       


Chain C from PDB  Type:PROTEIN  Length:167
 aligned with Q5LAA6_BACFN | Q5LAA6 from UniProtKB/TrEMBL  Length:170

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
         Q5LAA6_BACFN     2 AKESVKILQGKLDVKSLIDQLNAALSEEWLAYYQYWVGALVVEGAMRADVQGEFEEHAEEERHHAQLIADRIIELEGVPVLDPKKWFELARCKYDSPTAFDSVSLLNQNVSSERCAILRYQEIANFTNGKDYTTCDIAKHILAEEEEHEQDLQDYLTDIARMKESFL 168
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzb C   2 AKESVKILQGKLDVKSLIDQLNAALSEEWLAYYQYWVGALVVEGAMRADVQGEFEEHAEEERHHAQLIADRIIELEGVPVLDPKKWFELARCKYDSPTAFDSVSLLNQNVSSERCAILRYQEIANFTNGKDYTTCDIAKHILAEEEEHEQDLQDYLTDIARMKESFL 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       


Chain D from PDB  Type:PROTEIN  Length:167
 aligned with Q5LAA6_BACFN | Q5LAA6 from UniProtKB/TrEMBL  Length:170

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
         Q5LAA6_BACFN     2 AKESVKILQGKLDVKSLIDQLNAALSEEWLAYYQYWVGALVVEGAMRADVQGEFEEHAEEERHHAQLIADRIIELEGVPVLDPKKWFELARCKYDSPTAFDSVSLLNQNVSSERCAILRYQEIANFTNGKDYTTCDIAKHILAEEEEHEQDLQDYLTDIARMKESFL 168
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------Ferritin-2vzbD01 D:19-163                                                                                                                        ----- Pfam domains (1)
           Pfam domains (2) -----------------Ferritin-2vzbD02 D:19-163                                                                                                                        ----- Pfam domains (2)
           Pfam domains (3) -----------------Ferritin-2vzbD03 D:19-163                                                                                                                        ----- Pfam domains (3)
           Pfam domains (4) -----------------Ferritin-2vzbD04 D:19-163                                                                                                                        ----- Pfam domains (4)
         Sec.struct. author hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzb D   2 AKESVKILQGKLDVKSLIDQLNAALSEEWLAYYQYWVGALVVEGAMRADVQGEFEEHAEEERHHAQLIADRIIELEGVPVLDPKKWFELARCKYDSPTAFDSVSLLNQNVSSERCAILRYQEIANFTNGKDYTTCDIAKHILAEEEEHEQDLQDYLTDIARMKESFL 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 2VZB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5LAA6_BACFN | Q5LAA6)
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.
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.
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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