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(-) Description

Title :  CRYSTAL STRUCTURE OF TRIMERIC FRATAXIN FROM THE YEAST SACCHAROMYCES CEREVISIAE, COMPLEXED WITH COBALT
 
Authors :  C. A. G. Soderberg, S. Rajan, O. Gakh, C. Ta, G. Isaya, S. Al-Karadaghi
Date :  13 Aug 10  (Deposition) - 24 Aug 11  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Alpha/Beta Sandwich, Metallochaperone, Iron-Storage, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. A. Soderberg, A. V. Shkumatov, S. Rajan, O. Gakh, D. I. Svergun, G. Isaya, S. Al-Karadaghi
Oligomerization Propensity And Flexibility Of Yeast Frataxi Studied By X-Ray Crystallography And Small-Angle X-Ray Scattering.
J. Mol. Biol. V. 414 783 2011
PubMed-ID: 22051511  |  Reference-DOI: 10.1016/J.JMB.2011.10.034
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRATAXIN HOMOLOG, MITOCHONDRIAL
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 52-174
    GeneYFH1, YDL120W
    MutationYES
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymFRATAXIN HOMOLOG INTERMEDIATE FORM

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION

(-) Sites  (0, 0)

(no "Site" information available for 3OER)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OER)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OER)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OER)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FRATAXIN_2PS50810 Frataxin family profile.FRDA_YEAST66-174  1A:66-172
2FRATAXIN_1PS01344 Frataxin family signature.FRDA_YEAST120-134  1A:120-134
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FRATAXIN_2PS50810 Frataxin family profile.FRDA_YEAST66-174  3A:66-172
2FRATAXIN_1PS01344 Frataxin family signature.FRDA_YEAST120-134  3A:120-134

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDL120W1YDL120W.1IV:245923-246447525FRDA_YEAST1-1741741A:61-172112

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:112
 aligned with FRDA_YEAST | Q07540 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:112
                                    70        80        90       100       110       120       130       140       150       160       170  
           FRDA_YEAST    61 VPQEVLNLPLEKYHEEADDYLDHLLDSLEELSEAHPDCIPDVELSHGVMTLEIPAFGTYVINKQPPNKQIWLASPLSGPNRFDLLNGEWVSLRNGTKLTDILTEEVEKAISK 172
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.......hhhhhhhhhhhhhhhhhh......eeeeee..eeeeee...eeeeeeee....eeeeee...eeeeee.....eeee..eeehhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----FRATAXIN_2  PDB: A:66-172 UniProt: 66-174                                                                   PROSITE (1)
                PROSITE (2) -----------------------------------------------------------FRATAXIN_1     -------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:61-172 UniProt: 1-174 [INCOMPLETE]                                                              Transcript 1
                 3oer A  61 VPQEVLNLPLEKAHEEADDYLDHLLDSLEELSEAHPDCIPDVELSHGVMTLEIPAFGTYVINKQPPNKQIWLASPLSGPNRFDLLNGEWVSLRNGTKLTDILTEEVEKAISK 172
                                    70        80        90       100       110       120       130       140       150       160       170  

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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  (0, 0)

(no "SCOP Domain" information available for 3OER)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OER)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OER)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (FRDA_YEAST | Q07540)
molecular function
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0004322    ferroxidase activity    Catalysis of the reaction: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O.
    GO:0034986    iron chaperone activity    Assists in the delivery of iron ions to target proteins or compartments.
    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).
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0006749    glutathione metabolic process    The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
    GO:0006783    heme biosynthetic process    The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0016226    iron-sulfur cluster assembly    The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
    GO:0006121    mitochondrial electron transport, succinate to ubiquinone    The transfer of electrons from succinate to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex II.
    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:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:0010040    response to iron(II) ion    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.) as a result of an iron(II) ion stimulus.
    GO:0006979    response to oxidative stress    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.) as a result of 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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        FRDA_YEAST | Q075402fql 2ga5 3oeq 4ec2 5t0v 5tre

(-) Related Entries Specified in the PDB File

2fql 3oeq