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(-) Description

Title :  REDUCED BRIDGE-BROKEN YEAST CU/ZN SUPEROXIDE DISMUTASE LOW TEMPERATURE (-180C) STRUCTURE
 
Authors :  N. L. Ogihara, H. E. Parge, P. J. Hart, M. S. Weiss, J. S. Valentine, D. S. E J. A. Tainer
Date :  07 Dec 95  (Deposition) - 08 Mar 96  (Release) - 01 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Oxidoreductase (Superoxide Acceptor) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. L. Ogihara, H. E. Parge, P. J. Hart, M. S. Weiss, J. J. Goto, B. R. Crane J. Tsang, K. Slater, J. A. Roe, J. S. Valentine, D. Eisenberg, J. A. Tainer
Unusual Trigonal-Planar Copper Configuration Revealed In Th Atomic Structure Of Yeast Copper-Zinc Superoxide Dismutase.
Biochemistry V. 35 2316 1996
PubMed-ID: 8652572  |  Reference-DOI: 10.1021/BI951930B

(-) Compounds

Molecule 1 - CU/ZN SUPEROXIDE DISMUTASE
    ChainsA
    EC Number1.15.1.1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsLOW (93K) TEMPERATURE STRUCTURE WITH THE COPPER- IMIDAZOLATE BRIDGE BROKEN
    SynonymYEAST CU/ZN SOD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:46 , HIS A:48 , HIS A:63 , HIS A:120BINDING SITE FOR RESIDUE CU A 154
2AC2SOFTWAREHIS A:63 , HIS A:71 , HIS A:80 , ASP A:83BINDING SITE FOR RESIDUE ZN A 155
3CUUNKNOWNCU A:154 , HIS A:46 , HIS A:48 , HIS A:120NULL
4ZNUNKNOWNZN A:155 , HIS A:63 , HIS A:71 , HIS A:80 , ASP A:83NULL

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:57 -A:146

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JCV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_CU_ZN_1PS00087 Copper/Zinc superoxide dismutase signature 1.SODC_YEAST45-55  1A:44-54
2SOD_CU_ZN_2PS00332 Copper/Zinc superoxide dismutase signature 2.SODC_YEAST139-150  1A:138-149
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_CU_ZN_1PS00087 Copper/Zinc superoxide dismutase signature 1.SODC_YEAST45-55  2A:44-54
2SOD_CU_ZN_2PS00332 Copper/Zinc superoxide dismutase signature 2.SODC_YEAST139-150  2A:138-149

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJR104C1YJR104C.1X:623002-622538465SODC_YEAST1-1541541A:1-153153

(-) 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:153
 aligned with SODC_YEAST | P00445 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           SODC_YEAST     2 VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN 154
               SCOP domains d1jcva_ A: Cu,Zn superoxide dismutase, SOD                                                                                                                SCOP domains
               CATH domains 1jcvA00 A:1-153  [code=2.60.40.200, no name defined]                                                                                                      CATH domains
               Pfam domains --Sod_Cu-1jcvA01 A:3-149                                                                                                                             ---- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.......eeeeeeee......eeeeeee.........hhh.........................eee......eeeeeee..............eeee..............hhhh.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------SOD_CU_ZN_1-----------------------------------------------------------------------------------SOD_CU_ZN_2 ---- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-153 UniProt: 1-154 [INCOMPLETE]                                                                                                        Transcript 1
                 1jcv A   1 VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   

   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A   (SODC_YEAST | P00445)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) 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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004784    superoxide dismutase activity    Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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:0006878    cellular copper ion homeostasis    Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0006882    cellular zinc ion homeostasis    Any process involved in the maintenance of an internal steady state of zinc ions at the level of a cell.
    GO:0031505    fungal-type cell wall organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fungal-type cell wall.
    GO:1901856    negative regulation of cellular respiration    Any process that stops, prevents or reduces the frequency, rate or extent of cellular respiration.
    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:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0036091    positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress    Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    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: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:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    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.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

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        SODC_YEAST | P004451b4l 1b4t 1f18 1f1a 1f1d 1f1g 1jk9 1sdy 1yaz 1yso 2jcw

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