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(-) Description

Title :  THE CAMBIALISTIC SUPEROXIDE DISMUTASE (FE-SOD) OF P. SHERMANII COORDINATED BY AZIDE
 
Authors :  M. Schmidt, F. Parak
Date :  17 Sep 97  (Deposition) - 18 Mar 98  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase, Sod, Superoxide Dismutase, Propionibacterium Shermanii, Azide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schmidt, C. Scherk, O. Iakovleva, H. F. Nolting, B. Meier, F. Parak
The Structure Of The Azide Coordinated Superoxide Dismutase Of P. Shermanii Investigated By X-Ray Structure Analysis, Exafs, Mossbauer-And Epr Spectroscopy
Inorg. Chim. Acta. V. -276 65 1998
PubMed: search

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Organism Scientific: PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII
    Organism Taxid: 1752
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Strain: PZ3
    Synonym: SOD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1AZI2Ligand/IonAZIDE ION
2FE2Ligand/IonFE (III) ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1AZI4Ligand/IonAZIDE ION
2FE-1Ligand/IonFE (III) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:27 , HIS A:75 , ASP A:161 , HIS A:165 , AZI A:203 , HOH A:204BINDING SITE FOR RESIDUE FE A 202
2AC2SOFTWAREHIS A:27 , HIS A:31 , HIS A:32 , TYR A:35 , HIS A:75 , HIS A:165 , FE A:202BINDING SITE FOR RESIDUE AZI A 203
3AC3SOFTWAREHIS B:27 , HIS B:75 , ASP B:161 , HIS B:165 , AZI B:203 , HOH B:204BINDING SITE FOR RESIDUE FE B 202
4AC4SOFTWAREHIS B:27 , HIS B:31 , HIS B:32 , TYR B:35 , HIS B:75 , HIS B:165 , FE B:202 , HOH B:204BINDING SITE FOR RESIDUE AZI B 203
5FB1UNKNOWNHIS A:27 , HIS A:75 , HIS A:165 , ASP A:161 , AZI A:203 , HOH A:204FIRST COORDINATION SHELL OF THE IRON IN THE ACTIVE CENTER OF SUBUNIT A.
6FB2UNKNOWNHIS B:27 , HIS B:75 , HIS B:165 , ASP B:161 , AZI B:203 , HOH B:204FIRST COORDINATION SHELL OF THE IRON IN THE ACTIVE CENTER OF SUBUNIT B.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:16 -Pro A:17
2Glu B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_PROFR161-168
 		  2A:161-168
B:161-168
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_PROFR161-168
 		  4A:161-168
B:161-168

(-) Exons   (0, 0)

(no "Exon" information available for 1AVM)

(-) 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:201
 aligned with SODM_PROFR | P80293 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           SODM_PROFR     1 AVYTLPELPYDYSALEPYISGEIMELHHDKHHKAYVDGANTALDKLAEARDKADFGAINKLEKDLAFNLAGHVNHSVFWKNMAPKGSAPERPTDELGAAIDEFFGSFDNMKAQFTAAATGIQGSGWASLVWDPLGKRINTLQFYDHQNNLPAGSIPLLQLDMWEHAFYLQYKNVKGDYVKSWWNVVNWDDVALRFSEARVA 201
               SCOP domains d1avma1 A:1-86 Cambialistic superoxide dismutase                                      d1avma2 A:87-201 Cambialistic superoxide dismutase                                                                  SCOP domains
               CATH domains -------------------1avmA01 A:20-83 Fe,Mn superoxide dismutase (SOD) domain         ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhh..hhhhhhhhhhhhh.....eeeeeeee....eeeeeeee..........eeeeeee..hhhhhhhh...hhhhhhhh.....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1avm A   1 AVYTLPELPYDYSALEPYISGEIMELHHDKHHKAYVDGANTALDKLAEARDKADFGAINKLEKDLAFNLAGHVNHSVFWKNMAPKGSAPERPTDELGAAIDEFFGSFDNMKAQFTAAATGIQGSGWASLVWDPLGKRINTLQFYDHQNNLPAGSIPLLQLDMWEHAFYLQYKNVKGDYVKSWWNVVNWDDVALRFSEARVA 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 


Chain B from PDB  Type:PROTEIN  Length:201
 aligned with SODM_PROFR | P80293 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           SODM_PROFR     1 AVYTLPELPYDYSALEPYISGEIMELHHDKHHKAYVDGANTALDKLAEARDKADFGAINKLEKDLAFNLAGHVNHSVFWKNMAPKGSAPERPTDELGAAIDEFFGSFDNMKAQFTAAATGIQGSGWASLVWDPLGKRINTLQFYDHQNNLPAGSIPLLQLDMWEHAFYLQYKNVKGDYVKSWWNVVNWDDVALRFSEARVA 201
               SCOP domains d1avmb1 B:1-86 Cambialistic superoxide dismutase                                      d1avmb2 B:87-201 Cambialistic superoxide dismutase                                                                  SCOP domains
               CATH domains -------------------1avmB01 B:20-83 Fe,Mn superoxide dismutase (SOD) domain         ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhh..hhhhhhhhhhhhh.....eeeeeeee....eeeeeeee..........eeeeeee..hhhhhhhh...hhhhhhhh.....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1avm B   1 AVYTLPELPYDYSALEPYISGEIMELHHDKHHKAYVDGANTALDKLAEARDKADFGAINKLEKDLAFNLAGHVNHSVFWKNMAPKGSAPERPTDELGAAIDEFFGSFDNMKAQFTAAATGIQGSGWASLVWDPLGKRINTLQFYDHQNNLPAGSIPLLQLDMWEHAFYLQYKNVKGDYVKSWWNVVNWDDVALRFSEARVA 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 4)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AVM)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SODM_PROFR | P80293)
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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  1avm
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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
        SODM_PROFR | P80293: 1ar4 1ar5 1bs3 1bsm 1bt8

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