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(-) Description

Title :  CRYSTAL STRUCTURE OF THE Y34F MUTANT OF SACCHAROMYCES CEREVISIAE MANGANESE SUPEROXIDE DISMUTASE
 
Authors :  Y. Sheng, D. Cascio, J. S. Valentine
Date :  12 Mar 12  (Deposition) - 22 Aug 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Mn Superoxide Dismutase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Sheng, E. Butler Gralla, M. Schumacher, D. Cascio, D. E. Cabelli, J. Selverstone Valentine
Six-Coordinate Manganese(3+) In Catalysis By Yeast Manganes Superoxide Dismutase.
Proc. Natl. Acad. Sci. Usa V. 109 14314 2012
PubMed-ID: 22908245  |  Reference-DOI: 10.1073/PNAS.1212367109

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [MN], MITOCHONDRIAL
    Chains: A, B, C, D
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Plasmid: YEP352
    Expression System Strain: EG110
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Gene: SOD2, YHR008C
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: EG110

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 66)

Asymmetric/Biological Unit (2, 66)
No.NameCountTypeFull Name
1MLY62Mod. Amino AcidN-DIMETHYL-LYSINE
2MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:81 , ASP A:168 , HIS A:172 , HOH A:403BINDING SITE FOR RESIDUE MN A 301
2AC2SOFTWAREHIS B:26 , HIS B:81 , ASP B:168 , HIS B:172 , HOH B:401BINDING SITE FOR RESIDUE MN B 301
3AC3SOFTWAREHIS C:26 , HIS C:81 , ASP C:168 , HIS C:172 , HOH C:401BINDING SITE FOR RESIDUE MN C 301
4AC4SOFTWAREHIS D:26 , HIS D:81 , ASP D:168 , HIS D:172 , HOH D:401BINDING SITE FOR RESIDUE MN D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E4E)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:15 -Pro A:16
2Glu B:15 -Pro B:16
3Glu C:15 -Pro C:16
4Glu D:15 -Pro D:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E4E)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_YEAST194-201
 
 
 		  4A:168-175
B:168-175
C:168-175
D:168-175

(-) Exons   (0, 0)

(no "Exon" information available for 4E4E)

(-) 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:206
 aligned with SODM_YEAST | P00447 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:206
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226      
           SODM_YEAST    27 KVTLPDLKWDFGALEPYISGQINELHYTKHHQTYVNGFNTAVDQFQELSDLLAKEPSPANARKMIAIQQNIKFHGGGFTNHCLFWENLAPESQGGGEPPTGALAKAIDEQFGSLDELIKLTNTKLAGVQGSGWAFIVKNLSNGGKLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNKKADYFKAIWNVVNWKEASRRFDAGK 232
               SCOP domains d4e4ea1 A:1-90 automated matches                                                          d4e4ea2 A:91-206 automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeee........eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e4e A   1 kVTLPDLkWDFGALEPYISGQINELHYTkHHQTFVNGFNTAVDQFQELSDLLAkEPSPANARkMIAIQQNIkFHGGGFTNHCLFWENLAPESQGGGEPPTGALAkAIDEQFGSLDELIkLTNTkLAGVQGSGWAFIVkNLSNGGkLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNkkADYFkAIWNVVNWkEASRRFDAGk 206
                            |      |10        20        30        40        50   |    60  |     70 |      80        90       100    |  110       120   |   130       140    |  150       160       170       180||    |190     | 200     |
                            |      8-MLY               29-MLY                   54-MLY   63-MLY   72-MLY                          105-MLY       119-MLY|           138-MLY  |                                 181-MLY |      196-MLY   206-MLY
                            1-MLY                                                                                                                    124-MLY              145-MLY                              182-MLY|                   
                                                                                                                                                                                                                    187-MLY               


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with SODM_YEAST | P00447 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:207
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       
           SODM_YEAST    27 KVTLPDLKWDFGALEPYISGQINELHYTKHHQTYVNGFNTAVDQFQELSDLLAKEPSPANARKMIAIQQNIKFHGGGFTNHCLFWENLAPESQGGGEPPTGALAKAIDEQFGSLDELIKLTNTKLAGVQGSGWAFIVKNLSNGGKLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNKKADYFKAIWNVVNWKEASRRFDAGKI 233
               SCOP domains d4e4eb1 B:1-90 automated matches                                                          d4e4eb2 B:91-207 automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeee........eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e4e B   1 kVTLPDLkWDFGALEPYISGQINELHYTkHHQTFVNGFNTAVDQFQELSDLLAkEPSPANARkMIAIQQNIkFHGGGFTNHCLFWENLAPESQGGGEPPTGALAkAIDEQFGSLDELIkLTNTkLAGVQGSGWAFIVkNLSNGGkLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNkkADYFkAIWNVVNWkEASRRFDAGkI 207
                            |      |10        20        30        40        50   |    60  |     70 |      80        90       100    |  110       120   |   130       140    |  150       160       170       180||    |190     | 200     | 
                            |      8-MLY               29-MLY                   54-MLY   63-MLY   72-MLY                          105-MLY       119-MLY|           138-MLY  |                                 181-MLY |      196-MLY   206-MLY
                            1-MLY                                                                                                                    124-MLY              145-MLY                              182-MLY|                    
                                                                                                                                                                                                                    187-MLY                


Chain C from PDB  Type:PROTEIN  Length:205
 aligned with SODM_YEAST | P00447 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:205
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226     
           SODM_YEAST    27 KVTLPDLKWDFGALEPYISGQINELHYTKHHQTYVNGFNTAVDQFQELSDLLAKEPSPANARKMIAIQQNIKFHGGGFTNHCLFWENLAPESQGGGEPPTGALAKAIDEQFGSLDELIKLTNTKLAGVQGSGWAFIVKNLSNGGKLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNKKADYFKAIWNVVNWKEASRRFDAG 231
               SCOP domains d4e4ec1 C:1-90 automated matches                                                          d4e4ec2 C:91-205 automated matches                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeee........eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e4e C   1 kVTLPDLkWDFGALEPYISGQINELHYTkHHQTFVNGFNTAVDQFQELSDLLAkEPSPANARkMIAIQQNIkFHGGGFTNHCLFWENLAPESQGGGEPPTGALAkAIDEQFGSLDELIkLTNTkLAGVQGSGWAFIVkNLSNGGkLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNkkADYFkAIWNVVNWkEASRRFDAG 205
                            |      |10        20        30        40        50   |    60  |     70 |      80        90       100    |  110       120   |   130       140    |  150       160       170       180||    |190     | 200     
                            |      8-MLY               29-MLY                   54-MLY   63-MLY   72-MLY                          105-MLY       119-MLY|           138-MLY  |                                 181-MLY |      196-MLY     
                            1-MLY                                                                                                                    124-MLY              145-MLY                              182-MLY|                  
                                                                                                                                                                                                                    187-MLY              


Chain D from PDB  Type:PROTEIN  Length:203
 aligned with SODM_YEAST | P00447 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:203
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226   
           SODM_YEAST    27 KVTLPDLKWDFGALEPYISGQINELHYTKHHQTYVNGFNTAVDQFQELSDLLAKEPSPANARKMIAIQQNIKFHGGGFTNHCLFWENLAPESQGGGEPPTGALAKAIDEQFGSLDELIKLTNTKLAGVQGSGWAFIVKNLSNGGKLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNKKADYFKAIWNVVNWKEASRRFD 229
               SCOP domains d4e4ed1 D:1-90 automated matches                                                          d4e4ed2 D:91-203 automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeee........eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e4e D   1 kVTLPDLkWDFGALEPYISGQINELHYTkHHQTFVNGFNTAVDQFQELSDLLAkEPSPANARkMIAIQQNIkFHGGGFTNHCLFWENLAPESQGGGEPPTGALAkAIDEQFGSLDELIkLTNTkLAGVQGSGWAFIVkNLSNGGkLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNkkADYFkAIWNVVNWkEASRRFD 203
                            |      |10        20        30        40        50   |    60  |     70 |      80        90       100    |  110       120   |   130       140    |  150       160       170       180||    |190     | 200   
                            1-MLY  8-MLY               29-MLY                   54-MLY   63-MLY   72-MLY                          105-MLY       119-MLY|           138-MLY  |                                 181-MLY |      196-MLY   
                                                                                                                                                     124-MLY              145-MLY                              182-MLY|                
                                                                                                                                                                                                                    187-MLY
   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 4E4E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E4E)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SODM_YEAST | P00447)
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:0001324    age-dependent response to oxidative stress involved in chronological cell aging    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.) occurring in non-dividing cells as they age as a result of oxidative stress, where the change varies according to the age of the cell or organism.
    GO:0001320    age-dependent response to reactive oxygen species involved in chronological cell aging    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.) occurring in non-dividing cells as they age as a result of reactive oxygen species, where the change varies according to the age of the cell or organism.
    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:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
    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:0001302    replicative cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.
    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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  4e4e
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 Related Entries

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

UniProtKB/Swiss-Prot
        SODM_YEAST | P00447: 3bfr 3lsu 3rn4 4f6e

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4E4E)