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(-) Description

Title :  IRON-OXO CLUSTERS BIOMINERALIZING ON PROTEIN SURFACES. STRUCTURAL ANALYSIS OF H.SALINARUM DPSA IN ITS LOW AND HIGH IRON STATES
 
Authors :  K. Zeth, S. Offermann, L. O. Essen, D. Oesterhelt
Date :  09 Jun 04  (Deposition) - 19 Oct 04  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Dpsa, High Iron, Iron Cluster, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Zeth, S. Offermann, L. O. Essen, D. Oesterhelt
Iron-Oxo Clusters Biomineralizing On Protein Surfaces: Structural Analysis Of Halobacterium Salinarum Dpsa In Its Low- And High-Iron States.
Proc. Natl. Acad. Sci. Usa V. 101 13780 2004
PubMed-ID: 15365182  |  Reference-DOI: 10.1073/PNAS.0401821101

(-) Compounds

Molecule 1 - IRON-RICH DPSA-HOMOLOG PROTEIN
    Chains: A, B, C, D
    Organism Scientific: HALOBACTERIUM SALINARUM
    Organism Taxid: 2242
    Strain: TOM
    Synonym: BACTERIOFERRITIN DPSA

 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, 42)

Asymmetric Unit (3, 42)
No.NameCountTypeFull Name
1FE38Ligand/IonFE (III) ION
2NA2Ligand/IonSODIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NA-1Ligand/IonSODIUM ION
3SO46Ligand/IonSULFATE ION

(-) Sites  (41, 41)

Asymmetric Unit (41, 41)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:150 , ARG A:153 , HIS C:150 , ARG C:153 , HIS D:150 , ARG D:153 , HOH D:502BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWAREHIS B:150 , ARG B:153 , HOH B:338BINDING SITE FOR RESIDUE SO4 B 202
03AC3SOFTWAREGLU B:154 , FE B:319 , FE B:321BINDING SITE FOR RESIDUE FE B 301
04AC4SOFTWAREGLU A:154 , FE A:304 , HOH A:346 , GLU C:154 , FE C:303 , FE C:309 , GLU D:154BINDING SITE FOR RESIDUE FE A 302
05AC5SOFTWAREFE A:302 , FE A:304 , FE A:320 , GLU C:154 , FE C:309BINDING SITE FOR RESIDUE FE C 303
06AC6SOFTWAREGLU A:154 , FE A:302 , FE A:320 , HOH A:346 , FE C:303BINDING SITE FOR RESIDUE FE A 304
07AC7SOFTWAREHIS A:168 , GLN C:86 , GLU D:56BINDING SITE FOR RESIDUE FE C 305
08AC8SOFTWAREHIS A:164 , HIS A:168 , GLN C:86 , TRP D:53BINDING SITE FOR RESIDUE FE A 306
09AC9SOFTWAREFE C:308 , FE C:324BINDING SITE FOR RESIDUE FE C 307
10BC1SOFTWAREGLU C:75 , FE C:307 , FE C:324 , GLU D:75BINDING SITE FOR RESIDUE FE C 308
11BC2SOFTWAREFE A:302 , FE A:320 , HOH A:346 , FE C:303 , GLU D:154BINDING SITE FOR RESIDUE FE C 309
12BC3SOFTWAREGLU C:56 , HIS C:168 , GLN D:86BINDING SITE FOR RESIDUE FE D 310
13BC4SOFTWAREGLU A:75 , FE A:312 , FE A:325 , HOH A:348 , GLU B:75BINDING SITE FOR RESIDUE FE B 311
14BC5SOFTWAREGLU A:75 , FE A:325 , GLU B:72 , GLU B:75 , FE B:311BINDING SITE FOR RESIDUE FE A 312
15BC6SOFTWAREGLU A:56 , GLN B:86 , HIS B:168BINDING SITE FOR RESIDUE FE B 313
16BC7SOFTWAREGLN A:86 , GLU B:56 , HIS D:168BINDING SITE FOR RESIDUE FE A 314
17BC8SOFTWAREGLU C:171 , ASP C:172 , ASP D:25 , HOH D:506BINDING SITE FOR RESIDUE FE D 315
18BC9SOFTWAREGLU A:80 , GLU A:83BINDING SITE FOR RESIDUE FE A 316
19CC1SOFTWAREGLU C:80 , GLU C:83 , FE C:329 , HOH C:508BINDING SITE FOR RESIDUE FE C 317
20CC2SOFTWAREGLU B:80 , GLU B:83BINDING SITE FOR RESIDUE FE B 318
21CC3SOFTWAREFE B:301 , FE B:321BINDING SITE FOR RESIDUE FE B 319
22CC4SOFTWAREFE A:304 , FE C:303 , FE C:309BINDING SITE FOR RESIDUE FE A 320
23CC5SOFTWAREGLU B:154 , FE B:301 , FE B:319BINDING SITE FOR RESIDUE FE B 321
24CC6SOFTWAREASP A:172BINDING SITE FOR RESIDUE FE A 322
25CC7SOFTWAREGLU D:80BINDING SITE FOR RESIDUE FE D 323
26CC8SOFTWAREGLU C:75 , FE C:307 , FE C:308 , GLU D:75BINDING SITE FOR RESIDUE FE C 324
27CC9SOFTWAREFE A:312 , HOH A:348 , FE B:311BINDING SITE FOR RESIDUE FE A 325
28DC1SOFTWAREHIS C:52 , ASP D:79 , GLU D:83 , FE D:327BINDING SITE FOR RESIDUE FE D 326
29DC2SOFTWAREHIS C:64 , GLU D:83 , FE D:326BINDING SITE FOR RESIDUE FE D 327
30DC3SOFTWAREASP C:79 , GLU C:83 , FE C:329 , HIS D:52BINDING SITE FOR RESIDUE FE C 328
31DC4SOFTWAREGLU C:83 , FE C:317 , FE C:328 , HIS D:64BINDING SITE FOR RESIDUE FE C 329
32DC5SOFTWAREHIS A:52 , ASP B:79 , GLU B:83 , FE B:331BINDING SITE FOR RESIDUE FE B 330
33DC6SOFTWAREHIS A:64 , GLU B:83 , FE B:330BINDING SITE FOR RESIDUE FE B 331
34DC7SOFTWAREASP A:79 , GLU A:83 , HIS B:52BINDING SITE FOR RESIDUE FE A 332
35DC8SOFTWAREHIS B:64BINDING SITE FOR RESIDUE FE B 333
36DC9SOFTWARETRP C:53BINDING SITE FOR RESIDUE FE C 334
37EC1SOFTWARETRP B:53 , HIS D:164 , HIS D:168BINDING SITE FOR RESIDUE FE B 335
38EC2SOFTWAREGLU B:15 , GLU B:171 , HOH B:341BINDING SITE FOR RESIDUE FE B 336
39EC3SOFTWARETRP A:53 , HIS A:64BINDING SITE FOR RESIDUE FE A 338
40EC4SOFTWAREGLU A:59 , GLU D:59BINDING SITE FOR RESIDUE NA D 501
41EC5SOFTWAREALA C:58 , GLU C:59BINDING SITE FOR RESIDUE NA C 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TKO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TKO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TKO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TKO)

(-) Exons   (0, 0)

(no "Exon" information available for 1TKO)

(-) 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:180
 aligned with DPS_HALSA | Q9HMP7 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
            DPS_HALSA     2 STQKNARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
               SCOP domains d1tkoa_ A: Dodecameric ferritin homolog                                                                                                                                              SCOP domains
               CATH domains 1tkoA00 A:2-181  [code=1.20.1260.10, no name defined]                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tko A   2 STQKNARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with DPS_HALSA | Q9HMP7 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:175
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     
            DPS_HALSA     7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
               SCOP domains d1tkob_ B: Dodecameric ferritin homolog                                                                                                                                         SCOP domains
               CATH domains 1tkoB00 B:7-181  [code=1.20.1260.10, no name defined]                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tko B   7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     


Chain C from PDB  Type:PROTEIN  Length:175
 aligned with DPS_HALSA | Q9HMP7 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:175
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     
            DPS_HALSA     7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
               SCOP domains d1tkoc_ C: Dodecameric ferritin homolog                                                                                                                                         SCOP domains
               CATH domains 1tkoC00 C:7-181  [code=1.20.1260.10, no name defined]                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tko C   7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     


Chain D from PDB  Type:PROTEIN  Length:175
 aligned with DPS_HALSA | Q9HMP7 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:175
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     
            DPS_HALSA     7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
               SCOP domains d1tkod_ D: Dodecameric ferritin homolog                                                                                                                                         SCOP domains
               CATH domains 1tkoD00 D:7-181  [code=1.20.1260.10, no name defined]                                                                                                                           CATH domains
           Pfam domains (1) ------------------------Ferritin-1tkoD01 D:31-176                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) ------------------------Ferritin-1tkoD02 D:31-176                                                                                                                         ----- Pfam domains (2)
           Pfam domains (3) ------------------------Ferritin-1tkoD03 D:31-176                                                                                                                         ----- Pfam domains (3)
           Pfam domains (4) ------------------------Ferritin-1tkoD04 D:31-176                                                                                                                         ----- Pfam domains (4)
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tko D   7 ARATAGEVEGSDALRMDADRAEQCVDALNADLANVYVLYHQLKKHHWNVEGAEFRDLHLFLGEAAETAEEVADELAERVQALGGVPHASPETLQAEASVDVEDEDVYDIRTSLANDMAIYGDIIEATREHTELAENLGDHATAHMLREGLIELEDDAHHIEHYLEDDTLVTQGAL 181
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176
   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   (DPS_HALSA | Q9HMP7)
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: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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPS_HALSA | Q9HMP7: 1moj 1tjo 1tk6 1tkp

(-) Related Entries Specified in the PDB File

1moj FIRST HIGH RESOLUTION DATA
1tjo SECOND HIGH RESOLUTION, LOW IRON
1tk6 LOW IRON - SAD DATA COLLECTION AT THE IRON PEAK
1tkp