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(-) Description

Title :  Q69H-FESOD
 
Authors :  E. Yikilmaz, D. W. Rodgers, A. F. Miller
Date :  05 Apr 05  (Deposition) - 14 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  H-Bonding Redox Tuning Superoxide Dismutase Proton-Coupled Electron Transfer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Yikilmaz, D. W. Rodgers, A. F. Miller
The Crucial Importance Of Chemistry In The Structure-Function Link: Manipulating Hydrogen Bonding In Iron-Containing Superoxide Dismutase.
Biochemistry V. 45 1151 2006
PubMed-ID: 16430211  |  Reference-DOI: 10.1021/BI051495D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [FE]
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: QC774
    Expression System Taxid: 562
    Gene: SODB
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:73 , ASP A:156 , HIS A:160 , HOH A:196BINDING SITE FOR RESIDUE FE A 193
2AC2SOFTWAREHIS B:226 , HIS B:273 , ASP B:356 , HIS B:360 , HOH B:394BINDING SITE FOR RESIDUE FE B 393
3AC3SOFTWARESER A:51 , GLU A:54 , TRS B:1 , GLY B:249 , HOH B:429BINDING SITE FOR RESIDUE TRS A 194
4AC4SOFTWAREASP A:165 , HOH A:230 , HOH A:266 , HOH A:269 , GLU B:260BINDING SITE FOR RESIDUE TRS A 195
5AC5SOFTWAREGLY A:49 , TRS A:194 , GLY B:249 , LYS B:250 , SER B:251 , GLU B:254BINDING SITE FOR RESIDUE TRS B 1
6AC6SOFTWAREHOH A:372 , GLU B:221 , ARG B:257 , SER B:258 , SER B:259 , HOH B:513 , HOH B:560BINDING SITE FOR RESIDUE TRS B 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZA5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:15 -Pro A:16
2Ala B:215 -Pro B:216

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZA5)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_ECOLI157-164
 		  2A:156-163
B:356-363

(-) Exons   (0, 0)

(no "Exon" information available for 1ZA5)

(-) Sequences/Alignments

Asymmetric/Biological 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:192
 aligned with SODF_ECOLI | P0AGD3 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SODF_ECOLI     2 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAQVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 193
               SCOP domains d1za5a1 A:1-82 Fe superoxide dismutase (FeSOD)                                    d1za5a2 A:83-192 Fe superoxide dismutase (FeSOD)                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhh..eeeeeee.hhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1za5 A   1 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAHVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  


Chain B from PDB  Type:PROTEIN  Length:192
 aligned with SODF_ECOLI | P0AGD3 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SODF_ECOLI     2 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAQVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 193
               SCOP domains d1za5b1 B:201-282 Fe superoxide dismutase (FeSOD)                                 d1za5b2 B:283-392 Fe superoxide dismutase (FeSOD)                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Sod_Fe_N-1za5B03 B:201-281                                                       ----Sod_Fe_C-1za5B01 B:286-390                                                                               -- Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-1za5B04 B:201-281                                                       ----Sod_Fe_C-1za5B02 B:286-390                                                                               -- Pfam domains (2)
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhh..eeeeeee.hhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1za5 B 201 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAHVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 392
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZA5)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Sod_Fe_C] (46)
(-)
Clan: no clan defined [family: Sod_Fe_N] (46)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SODF_ECOLI | P0AGD3)
molecular function
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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:0004784    superoxide dismutase activity    Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
    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:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
    GO:0000303    response to superoxide    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 superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.
    GO:0006801    superoxide metabolic process    The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  1za5
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  SODF_ECOLI | P0AGD3
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  1.15.1.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        SODF_ECOLI | P0AGD3: 1isa 1isb 1isc 2bkb 2nyb

(-) Related Entries Specified in the PDB File

1isa FESOD, REDUCED
1isb FESOD, OXIDIZED