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(-) Description

Title :  ASCORBATE PEROXIDASE FROM SOYBEAN CYTOSOL
 
Authors :  K. H. Sharp, E. L. Raven, P. C. E. Moody
Date :  13 Jan 03  (Deposition) - 20 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Heme Peroxidase, Peroxide Scavenge, Ascorbate Peroxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Sharp, M. Mewies, P. C. E. Moody, E. L. Raven
Crystal Structure Of The Ascorbate Peroxidase-Ascorbate Complex
Nat. Struct. Biol. V. 10 303 2003
PubMed-ID: 12640445  |  Reference-DOI: 10.1038/NSB913

(-) Compounds

Molecule 1 - ASCORBATE PEROXIDASE
    Chains: A
    EC Number: 1.11.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAPX4
    Expression System Strain: SG13009
    Expression System Taxid: 562
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Other Details: N-TERMINAL 6-HIS TAG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:127 , ARG A:130 , HOH A:2474 , HOH A:2475 , HOH A:2477 , HOH A:2478BINDING SITE FOR RESIDUE SO4 A 252
2AC2SOFTWAREPRO A:34 , TRP A:41 , PRO A:132 , ALA A:134 , PHE A:145 , LEU A:159 , SER A:160 , GLY A:162 , HIS A:163 , ILE A:165 , GLY A:166 , ALA A:167 , ALA A:168 , HIS A:169 , ARG A:172 , SER A:173 , TRP A:179 , LEU A:205 , SER A:207 , TYR A:235 , HOH A:2470 , HOH A:2471 , HOH A:2472 , HOH A:2473BINDING SITE FOR RESIDUE HEM A 251

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OAG)

(-) 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:249
 aligned with Q43758_SOYBN | Q43758 from UniProtKB/TrEMBL  Length:250

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
         Q43758_SOYBN     2 GKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADA 250
               SCOP domains d1oaga_ A: Ascorbate peroxidase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1oagA01 A:2-131,A:239-250  [code=1.10.520.10, no name defined]                                                                    1oagA02 A:132-238 Peroxidase, domain 2                                                                     1oagA01      CATH domains
               Pfam domains --------peroxidase-1oagA01 A:10-227                                                                                                                                                                                               ----------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh............................hhhhhhhhhh.....hhhhhhhhhhhhhh.ee........ee.........hhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oag A   2 GKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADA 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: peroxidase] (92)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q43758_SOYBN | Q43758)
molecular function
    GO:0016688    L-ascorbate peroxidase activity    Catalysis of the reaction: L-ascorbate + hydrogen peroxide = dehydroascorbate + 2 H2O.
    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: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: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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  1oag
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  1.11.1.11
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 Related Entries

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

UniProtKB/TrEMBL
        Q43758_SOYBN | Q43758: 1oaf 1v0h 2cl4 2ggn 2ghc 2ghd 2ghe 2ghh 2ghk 2vcf 2vcn 2vcs 2vnx 2vnz 2vo2 2wd4 2xi6 2xif 2xih 2xj6 2y6a 2y6b 3zcg 3zch 3zcy 5jpr 5jqr 5l86

(-) Related Entries Specified in the PDB File

1oaf ASCOBATE PEROXIDASE FROM SOYBEAN CYTOSOL IN COMPLEX WITH ASCORBATE