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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE EUKARYOTIC FESOD FROM VIGNA UNGUICULATA SUGGESTS A NEW ENZYMATIC MECHANISM
 
Authors :  I. G. Munoz, J. F. Moran, M. Becana, G. Montoya
Date :  10 Sep 03  (Deposition) - 27 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  X
Keywords :  Oxidoreductase, Eukaryotic, Superoxide Dismutase, Metalloprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. G. Munoz, J. F. Moran, M. Becana, G. Montoya
The Crystal Structure Of An Eukaryotic Iron Superoxide Dismutase Suggests Intersubunit Cooperation During Catalysis
Protein Sci. V. 14 387 2005
PubMed-ID: 15659371  |  Reference-DOI: 10.1110/PS.04979505

(-) Compounds

Molecule 1 - IRON SUPEROXIDE DISMUTASE
    Cellular Location: CYTOSOL
    Chains: X
    EC Number: 1.15.1.1
    Organism Common: COWPEA
    Organism Scientific: VIGNA UNGUICULATA
    Organism Taxid: 3917
    Strain: VUFESOD
    Synonym: SUPEROXIDE DISMUTASE [MN/FE]
    Tissue: LEGUME ROOT NODULES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS X:43 , HIS X:95 , ASP X:195 , HIS X:199 , HOH X:2141BINDING SITE FOR RESIDUE FE X1239

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu X:32 -Pro X:33
2Glu X:167 -Asp X:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UNF)

(-) 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 X from PDB  Type:PROTEIN  Length:214
 aligned with Q9M7R2_VIGUN | Q9M7R2 from UniProtKB/TrEMBL  Length:245

    Alignment length:225
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
         Q9M7R2_VIGUN    21 KVNAKFELKPPPYPLNGLEPVMSQQTLEFHWGKHHRTYVENLKKQVVGTELDGKSLEEIIVTAYNKGDILPAFNNAAQVWNHDFFWECMKPGGGGKPSGELLELIERDFGSFEKFLDEFKAAAATQFGSGWAWLAYKASKLDGENAANPPSADEDNKLVVIKSPNAVNPLVWGGYYPLLTIDVWEHAYYLDFQNRRPDYISVFMDKLVSWDAVSSRLEQAKALSA 245
               SCOP domains d1unfx1 X:14-104 Fe superoxide dismutase (FeSO  D)                                         d1unfx2 X:105-238 Fe superoxide dismutase (FeSOD)                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Sod_Fe_N-1unfX02 X:18-103                                                             ----Sod_Fe_C-1unfX01 X:108-230                                                                                                 -------- Pfam domains
         Sec.struct. author ......................hhhhhhhhh.hhhhhhhhhhhhhh--......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhh---------.....eeeeeeee...hhhhh..eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1unf X  14 KVNAKFELKPPPYPLNGLEPVMSQQTLEFHWGKHHRTYVENLKKQV--TELDGKSLEEIIVTAYNKGDILPAFNNAAQVWNHDFFWECMKPGGGGKPSGELLELIERDFGSFEKFLDEFKAAAATQFGSGWAWLAYKASKLD---------ADEDNKLVVIKSPNAVNPLVWGGYYPLLTIDVWEHAYYLDFQNRRPDYISVFMDKLVSWDAVSSRLEQAKALSA 238
                                    23        33        43        53     |  63        73        83        93       103       113       123       133       143       153 |       - |     173       183       193       203       213       223       233     
                                                                        59 62                                                                                          155       165
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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  (2, 2)

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 1UNF)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (Q9M7R2_VIGUN | Q9M7R2)
molecular function
    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:0006801    superoxide metabolic process    The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.

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