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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI MITOCHONDRIAL IRON SUPEROXIDE DISMUTASE
 
Authors :  N. Larrieux, A. Buschiazzo
Date :  23 Feb 12  (Deposition) - 27 Mar 13  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Iron Superoxide Dismutase, Mitochondrial, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Martinez, G. Peluffo, A. A. Petruk, M. Hugo, D. Pineyro, V. Demicheli, D. M. Moreno, A. Lima, C. Batthyany, R. Duran, C. Robello M. A. Marti, N. Larrieux, A. Buschiazzo, M. Trujillo, R. Radi, L. Piacenza
Structural And Molecular Basis Of The Peroxynitrite-Mediate Nitration And Inactivation Of Trypanosoma Cruzi Iron-Superoxide Dismutases (Fe-Sods) A And B: Disparate Susceptibilities Due To The Repair Of Tyr35 Radical By Cys8 In Fe-Sodb Through Intramolecular Electron Transfer.
J. Biol. Chem. V. 289 12760 2014
PubMed-ID: 24616096  |  Reference-DOI: 10.1074/JBC.M113.545590

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TC00.1047053509775.40
    Organism Scientific: TRYPANOSOMA CRUZI
    Organism Taxid: 353153
    Strain: CL BRENER

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:28 , HIS A:79 , ASP A:163 , HIS A:167 , HOH A:402BINDING SITE FOR RESIDUE FE A 301
2AC2SOFTWAREHIS B:28 , HIS B:79 , ASP B:163 , HIS B:167 , HOH B:405BINDING SITE FOR RESIDUE FE B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:1 -Pro A:2
2Ala A:17 -Pro A:18
3Ala B:1 -Pro B:2
4Ala B:17 -Pro B:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DVH)

(-) Exons   (0, 0)

(no "Exon" information available for 4DVH)

(-) 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:203
 aligned with Q4DCQ3_TRYCC | Q4DCQ3 from UniProtKB/TrEMBL  Length:233

    Alignment length:203
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
         Q4DCQ3_TRYCC    31 GAPAELPKLGFNWKDGCAPVFSPRQMELHYTKHHKAYVDKLNALAGTTYDGKSIEEIILAVANDAEKKGLFNQAAQHFNHTFYFRCITPNGKAMPKSLESAVTAQFGSVEQFKDAFVQAGVNNFGSGWTWLCVDPSNKNQLVIDNTSNAGCPLTKGLRPVLAVDVWEHAYYKDFENRRPDYLKEIWSVIDWEFVAKMHAQAIK 233
               SCOP domains d4dvha1 A:0-88 automated matches                                                         d4dvha2 A:89-202 automated matches                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.......eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dvh A   0 HAPAELPKLGFNWKDGCAPVFSPRQMELHYTKHHKAYVDKLNALAGTTYDGKSIEEIILAVANDAEKKGLFNQAAQHFNHTFYFRCITPNGKAMPKSLESAVTAQFGSVEQFKDAFVQAGVNNFGSGWTWLCVDPSNKNQLVIDNTSNAGCPLTKGLRPVLAVDVWEHAYYKDFENRRPDYLKEIWSVIDWEFVAKMHAQAIK 202
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with Q4DCQ3_TRYCC | Q4DCQ3 from UniProtKB/TrEMBL  Length:233

    Alignment length:203
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229   
         Q4DCQ3_TRYCC    30 SGAPAELPKLGFNWKDGCAPVFSPRQMELHYTKHHKAYVDKLNALAGTTYDGKSIEEIILAVANDAEKKGLFNQAAQHFNHTFYFRCITPNGKAMPKSLESAVTAQFGSVEQFKDAFVQAGVNNFGSGWTWLCVDPSNKNQLVIDNTSNAGCPLTKGLRPVLAVDVWEHAYYKDFENRRPDYLKEIWSVIDWEFVAKMHAQAI 232
               SCOP domains d4dvhb1 B:-1-88 automated matches                                                         d4dvhb2 B:89-201 automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.......eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dvh B  -1 HHAPAELPKLGFNWKDGCAPVFSPRQMELHYTKHHKAYVDKLNALAGTTYDGKSIEEIILAVANDAEKKGLFNQAAQHFNHTFYFRCITPNGKAMPKSLESAVTAQFGSVEQFKDAFVQAGVNNFGSGWTWLCVDPSNKNQLVIDNTSNAGCPLTKGLRPVLAVDVWEHAYYKDFENRRPDYLKEIWSVIDWEFVAKMHAQAI 201
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198
   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/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 4DVH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q4DCQ3_TRYCC | Q4DCQ3)
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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  4dvh
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  1.15.1.1
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 Related Entries

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        Q4DCQ3_TRYCC | Q4DCQ3: 4h3e

(-) Related Entries Specified in the PDB File

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