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(-) Description

Title :  CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS MNSOD
 
Authors :  S. Fluckiger, P. R. E. Mittl, L. Scapozza, H. Fijten, G. Folkers, M. G. Grutter, K. Blaser, R. Crameri
Date :  07 Dec 01  (Deposition) - 28 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,X,Y
Keywords :  Homotetramer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Fluckiger, P. R. Mittl, L. Scapozza, H. Fijten, G. Folkers, M. G. Grutter, K. Blaser, R. Crameri
Comparison Of The Crystal Structures Of The Human Manganese Superoxide Dismutase And The Homologous Aspergillus Fumigatus Allergen At 2-A Resolution.
J. Immunol. V. 168 1267 2002
PubMed-ID: 11801664
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANGANESE SUPEROXIDE DISMUTASE
    Chains: A, B, X, Y
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PQE16
    Organism Scientific: ASPERGILLUS FUMIGATUS
    Organism Taxid: 5085
    Synonym: MNSOD

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:40 , HIS A:88 , ASP A:174 , HIS A:178 , HOH A:2005BINDING SITE FOR RESIDUE MN A 2001
2AC2SOFTWAREHIS B:40 , HIS B:88 , ASP B:174 , HIS B:178 , HOH B:2003BINDING SITE FOR RESIDUE MN B 2002
3AC3SOFTWAREHIS X:40 , HIS X:88 , ASP X:174 , HIS X:178 , HOH X:2004BINDING SITE FOR RESIDUE MN X 2003
4AC4SOFTWAREHIS Y:40 , HIS Y:88 , ASP Y:174 , HIS Y:178 , HOH Y:2006BINDING SITE FOR RESIDUE MN Y 2004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gln A:29 -Pro A:30
2Gln B:29 -Pro B:30
3Gln X:29 -Pro X:30
4Gln Y:29 -Pro Y:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_ASPFU163-170
 
 
 		  4A:174-181
B:174-181
X:174-181
Y:174-181

(-) Exons   (0, 0)

(no "Exon" information available for 1KKC)

(-) 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:200
 aligned with SODM_ASPFU | Q92450 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:200
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
           SODM_ASPFU     3 QQYTLPPLPYPYDALQPYISQQIMELHHKKHHQTYVNGLNAALEAQKKAAEANDVPKLVSVQQAIKFNGGGHINHSLFWKNLAPEKSGGGKIDQAPVLKAAIEQRWGSFDKFKDAFNTTLLGIQGSGWGWLVTDGPKGKLDITTTHDQDPVTGAAPVFGVDMWEHAYYLQYLNDKASYAKGIWNVINWAEAENRYIAGDK 202
               SCOP domains d1kkca1 A:14-97 Mn superoxide dismutase (MnSOD)                                     d1kkca2 A:98-213 Mn superoxide dismutase (MnSOD)                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kkc A  14 QQYTLPPLPYPYDALQPYISQQIMELHHKKHHQTYVNGLNAALEAQKKAAEATDVPKLVSVQQAIKFNGGGHINHSLFWKNLAPEKSGGGKIDQAPVLKAAIEQRWGSFDKFKDAFNTTLLGIQGSGWGWLVTDGPKGKLDITTTHDQDPVTGAAPVFGVDMWEHAYYLQYLNDKASYAKGIWNVINWAEAENRYIAGDK 213
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213


Chain B from PDB  Type:PROTEIN  Length:199
 aligned with SODM_ASPFU | Q92450 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:199
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193         
           SODM_ASPFU     4 QYTLPPLPYPYDALQPYISQQIMELHHKKHHQTYVNGLNAALEAQKKAAEANDVPKLVSVQQAIKFNGGGHINHSLFWKNLAPEKSGGGKIDQAPVLKAAIEQRWGSFDKFKDAFNTTLLGIQGSGWGWLVTDGPKGKLDITTTHDQDPVTGAAPVFGVDMWEHAYYLQYLNDKASYAKGIWNVINWAEAENRYIAGDK 202
               SCOP domains d1kkcb1 B:15-97 Mn superoxide dismutase (MnSOD)                                    d1kkcb2 B:98-213 Mn superoxide dismutase (MnSOD)                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kkc B  15 QYTLPPLPYPYDALQPYISQQIMELHHKKHHQTYVNGLNAALEAQKKAAEATDVPKLVSVQQAIKFNGGGHINHSLFWKNLAPEKSGGGKIDQAPVLKAAIEQRWGSFDKFKDAFNTTLLGIQGSGWGWLVTDGPKGKLDITTTHDQDPVTGAAPVFGVDMWEHAYYLQYLNDKASYAKGIWNVINWAEAENRYIAGDK 213
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         


Chain X from PDB  Type:PROTEIN  Length:200
 aligned with SODM_ASPFU | Q92450 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:200
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203
           SODM_ASPFU     4 QYTLPPLPYPYDALQPYISQQIMELHHKKHHQTYVNGLNAALEAQKKAAEANDVPKLVSVQQAIKFNGGGHINHSLFWKNLAPEKSGGGKIDQAPVLKAAIEQRWGSFDKFKDAFNTTLLGIQGSGWGWLVTDGPKGKLDITTTHDQDPVTGAAPVFGVDMWEHAYYLQYLNDKASYAKGIWNVINWAEAENRYIAGDKG 203
               SCOP domains d1kkcx1 X:15-97 Mn superoxide dismutase (MnSOD)                                    d1kkcx2 X:98-214 Mn superoxide dismutase (MnSOD)                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kkc X  15 QYTLPPLPYPYDALQPYISQQIMELHHKKHHQTYVNGLNAALEAQKKAAEATDVPKLVSVQQAIKFNGGGHINHSLFWKNLAPEKSGGGKIDQAPVLKAAIEQRWGSFDKFKDAFNTTLLGIQGSGWGWLVTDGPKGKLDITTTHDQDPVTGAAPVFGVDMWEHAYYLQYLNDKASYAKGIWNVINWAEAENRYIAGDKG 214
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214


Chain Y from PDB  Type:PROTEIN  Length:200
 aligned with SODM_ASPFU | Q92450 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:200
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
           SODM_ASPFU     3 QQYTLPPLPYPYDALQPYISQQIMELHHKKHHQTYVNGLNAALEAQKKAAEANDVPKLVSVQQAIKFNGGGHINHSLFWKNLAPEKSGGGKIDQAPVLKAAIEQRWGSFDKFKDAFNTTLLGIQGSGWGWLVTDGPKGKLDITTTHDQDPVTGAAPVFGVDMWEHAYYLQYLNDKASYAKGIWNVINWAEAENRYIAGDK 202
               SCOP domains d1kkcy1 Y:14-97 Mn superoxide dismutase (MnSOD)                                     d1kkcy2 Y:98-213 Mn superoxide dismutase (MnSOD)                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Sod_Fe_N-1kkcY05 Y:15-96                                                          ----------Sod_Fe_C-1kkcY01 Y:107-208                                                                            ----- Pfam domains (1)
           Pfam domains (2) -Sod_Fe_N-1kkcY06 Y:15-96                                                          ----------Sod_Fe_C-1kkcY02 Y:107-208                                                                            ----- Pfam domains (2)
           Pfam domains (3) -Sod_Fe_N-1kkcY07 Y:15-96                                                          ----------Sod_Fe_C-1kkcY03 Y:107-208                                                                            ----- Pfam domains (3)
           Pfam domains (4) -Sod_Fe_N-1kkcY08 Y:15-96                                                          ----------Sod_Fe_C-1kkcY04 Y:107-208                                                                            ----- Pfam domains (4)
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kkc Y  14 QQYTLPPLPYPYDALQPYISQQIMELHHKKHHQTYVNGLNAALEAQKKAAEATDVPKLVSVQQAIKFNGGGHINHSLFWKNLAPEKSGGGKIDQAPVLKAAIEQRWGSFDKFKDAFNTTLLGIQGSGWGWLVTDGPKGKLDITTTHDQDPVTGAAPVFGVDMWEHAYYLQYLNDKASYAKGIWNVINWAEAENRYIAGDK 213
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213
   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, 8)

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 1KKC)

(-) Pfam Domains  (2, 8)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,X,Y   (SODM_ASPFU | Q92450)
molecular function
    GO:0019863    IgE binding    Interacting selectively and non-covalently with an immunoglobulin of the IgE isotype.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) 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: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:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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  1kkc
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  SODM_ASPFU | Q92450
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  1.15.1.1
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