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(-) Description

Title :  ASCOBATE PEROXIDASE FROM SOYBEAN CYTOSOL IN COMPLEX WITH SALICYLHYDROXAMIC ACID
 
Authors :  K. H. Sharp, E. L. Raven, P. C. E. Moody
Date :  29 Mar 04  (Deposition) - 23 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.46
Chains :  Asym./Biol. Unit :  X
Keywords :  Oxidoreductase, Heme Peroxidase, Peroxide Scavenge, Ascorbate Peroxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Sharp, P. C. E. Moody, K. A. Brown, E. L. Raven
Crystal Structure Of The Ascorbate Peroxidase-Salicylhydroxamic Acid Complex
Biochemistry V. 43 8644 2004
PubMed-ID: 15236572  |  Reference-DOI: 10.1021/BI049343Q

(-) Compounds

Molecule 1 - ASCORBATE PEROXIDASE
    Chains: X
    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: SALICYLHYDROXAMIC ACID COMPLEX
    Other Details - Source: N-TERMINAL 6-HIS TAG
    Strain: SG13009

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA1Ligand/IonSODIUM ION
3SHA1Ligand/IonSALICYLHYDROXAMIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR X:164 , THR X:180 , ASN X:182 , ILE X:185 , HOH X:2319 , HOH X:2324BINDING SITE FOR RESIDUE NA X 252
2AC2SOFTWAREPRO X:34 , TRP X:41 , PRO X:132 , ALA X:134 , LEU X:159 , SER X:160 , GLY X:162 , HIS X:163 , ILE X:165 , GLY X:166 , ALA X:167 , ALA X:168 , HIS X:169 , ARG X:172 , SER X:173 , TRP X:179 , LEU X:205 , SER X:207 , TYR X:235 , SHA X:253 , HOH X:2401 , HOH X:2402 , HOH X:2403BINDING SITE FOR RESIDUE HEM X 251
3AC3SOFTWAREARG X:38 , TRP X:41 , HIS X:42 , ALA X:70 , PRO X:132 , HEM X:251BINDING SITE FOR RESIDUE SHA X 253

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V0H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V0H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V0H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V0H)

(-) Exons   (0, 0)

(no "Exon" information available for 1V0H)

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

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
         Q43758_SOYBN     1 MGKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFAD 249
               SCOP domains d1v0hx_ X: Ascorbate peroxidase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1v0hX01 X:1-131,X:239-249  [code=1.10.520.10, no name defined]                                                                     1v0hX02 X:132-238 Peroxidase, domain 2                                                                     1v0hX01     CATH domains
               Pfam domains ---------peroxidase-1v0hX01 X:10-227                                                                                                                                                                                               ---------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh............................hhhhhhhhhh.....hhhhhhhhhhhhhh.ee........ee.........hhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v0h X   1 SGKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFAD 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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 X   (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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 Related Entries

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

UniProtKB/TrEMBL
        Q43758_SOYBN | Q43758: 1oaf 1oag 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
1oag ASCOBATE PEROXIDASE FROM SOYBEAN CYTOSOL