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(-) Description

Title :  CRYSTAL STRUCTURE OF CHLOROPLASTIC ASCORBATE PEROXIDASE FROM TOBACCO PLANTS AND STRUCTURAL INSIGHTS FOR ITS INSTABILITY
 
Authors :  K. Wada, T. Tada, Y. Nakamura
Date :  03 Sep 02  (Deposition) - 03 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Ascorbate, Peroxidase, Hydrogen Peroxide, Tobacco Plant, Stromal Ascorbate Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Wada, T. Tada, Y. Nakamura, T. Ishikawa, Y. Yabuta, K. Yoshimura, S. Shigeoka, K. Nishimura
Crystal Structure Of Chloroplastic Ascorbate Peroxidase From Tobacco Plants And Structural Insights Into Its Instability
J. Biochem. (Tokyo) V. 134 239 2003
PubMed-ID: 12966073  |  Reference-DOI: 10.1093/JB/MVG136
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHLOROPLASTIC ASCORBATE PEROXIDASE
    Chains: A
    EC Number: 1.11.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: COMMON TOBACCO
    Organism Scientific: NICOTIANA TABACUM
    Organism Taxid: 4097
    Synonym: STROMAL ASCORBATE PEROXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA2Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:164 , THR A:196 , GLN A:198 , LYS A:201 , HOH A:312BINDING SITE FOR RESIDUE NA A 297
2AC2SOFTWAREASP A:35 , GLY A:51 , ASN A:53 , SER A:55 , HOH A:306BINDING SITE FOR RESIDUE NA A 298
3AC3SOFTWAREPRO A:26 , ARG A:30 , TRP A:33 , PRO A:131 , ASP A:132 , ALA A:133 , LEU A:142 , PHE A:146 , LEU A:159 , ALA A:162 , HIS A:163 , GLY A:166 , ARG A:167 , SER A:168 , ARG A:169 , ARG A:172 , SER A:173 , TRP A:195 , THR A:223 , TYR A:251 , HOH A:299 , HOH A:305 , HOH A:325 , HOH A:363BINDING SITE FOR RESIDUE HEM A 296

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Trp A:46 -Pro A:47
2Gly A:186 -Pro A:187
3Gly A:266 -Pro A:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IYN)

(-) Exons   (0, 0)

(no "Exon" information available for 1IYN)

(-) 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:275
 aligned with Q8LNY5_TOBAC | Q8LNY5 from UniProtKB/TrEMBL  Length:295

    Alignment length:275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     
         Q8LNY5_TOBAC     1 AASDSAQLKSAREDIKELLKTKFCHPIMVRLGWHDAGTYNKNIEEWPQRGGANGSLRFDVELKHGANAGLVNALNLLKPIKDKYSGVTYADLFQLASATAIEEAGGPKIPMKYGRVDVTEPEQCPEEGRLPDAGPPSPAQHLRDVFYRMGLNDKEIVALSGAHTLGRSRPDRSGWGKPETKYTKDGPGAPGGQSWTAQWLKFDNSYFKDIKERRDEDLLVLPTDAALFEDPSFKVYAEKYAADPEAFFKDYAEAHAKLSNLGAKFGPAEGFSLEG 275
               SCOP domains d1iyna_ A: Ascorbate peroxidase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1iynA01 A:1-130,A:255-275  [code=1.10.520.10, no name defined]                                                                    1iynA02 A:131-254 Peroxidase, domain 2                                                                                      1iynA01               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...............hhhhh............hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee........................ee.........hhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iyn A   1 AASDSAQLKSAREDIKELLKTKFCHPIMVRLGWHDAGTYNKNIEEWPQRGGANGSLRFDVELKHGANAGLVNALNLLKPIKDKYSGVTYADLFQLASATAIEEAGGPKIPMKYGRVDVTEPEQCPEEGRLPDAGPPSPAQHLRDVFYRMGLNDKEIVALSGAHTLGRSRPDRSGWGKPETKYTKDGPGAPGGQSWTAQWLKFDNSYFKDIKERRDEDLLVLPTDAALFEDPSFKVYAEKYAADPEAFFKDYAEAHAKLSNLGAKFGPAEGFSLEG 275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IYN)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8LNY5_TOBAC | Q8LNY5)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    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: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: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.

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