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(-) Description

Title :  ASCORBATE PEROXIDASE R172A MUTANT
 
Authors :  L. Ghamsari, I. K. Macdonald, P. C. E. Moody
Date :  25 Apr 06  (Deposition) - 06 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  X
Keywords :  Peroxide Scavenge, Ascorbate Peroxidase, Oxidoreductase, Hem Peroxidase, Iron, Heme, Peroxidase, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. K. Macdonald, S. K. Badyal, L. Ghamsari, P. C. E. Moody, E. L. Raven
Interaction Of Ascorbate Peroxidase With Substrates: A Mechanistic And Structural Analysis.
Biochemistry V. 45 7808 2006
PubMed-ID: 16784232  |  Reference-DOI: 10.1021/BI0606849

(-) Compounds

Molecule 1 - ASCORBATE PEROXIDASE
    ChainsX
    EC Number1.11.1.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainSG
    Expression System Taxid562
    Expression System VectorPQE30
    MutationYES
    Organism CommonSOYBEAN
    Organism ScientificGLYCINE MAX
    Organism Taxid3847
    SynonymCYTOSOLIC ASCORBATE PEROXIDASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA1Ligand/IonSODIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR X:164 , THR X:180 , ASN X:182 , ILE X:185 , ASP X:187BINDING SITE FOR RESIDUE NA X 252
2AC2SOFTWARELYS X:136 , GLY X:137 , SER X:138 , ASP X:139 , HIS X:140 , HOH X:2325 , HOH X:2326 , HOH X:2327 , HOH X:2328BINDING SITE FOR RESIDUE SO4 X4770
3AC3SOFTWAREPRO X:127 , ARG X:130 , HOH X:2189 , HOH X:2329 , HOH X:2330 , HOH X:2331BINDING SITE FOR RESIDUE SO4 X4771
4AC4SOFTWAREPRO X:34 , TRP X:41 , PRO X:132 , ALA X:134 , LEU X:141 , PHE X:145 , 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 , ALA X:172 , SER X:173 , TRP X:179 , LEU X:205 , SER X:207 , TYR X:235 , HOH X:2072 , HOH X:2322 , HOH X:2323 , HOH X:2324BINDING SITE FOR RESIDUE HEM X 251

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CL4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CL4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CL4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CL4)

(-) Exons   (0, 0)

(no "Exon" information available for 2CL4)

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

    Alignment length:250
                                    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
         Q43758_SOYBN     1 MGKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADA 250
               SCOP domains d2cl4x_ X: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains 2cl4X01 X:1-131,X:239-250  [code=1.10.520.10, no name defined]                                                                     2cl4X02 X:132-238 Peroxidase, domain 2                                                                     2cl4X01      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh............................hhhhhhhhhh.....hhhhhhhhhhhhhh.ee........ee.........hhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cl4 X   1 SGKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKEASGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADA 250
                                    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

   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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CL4)

(-) 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 | Q437581oaf 1oag 1v0h 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
1v0h ASCOBATE PEROXIDASE FROM SOYBEAN CYTOSOL IN COMPLEX WITH SALICYLHYDROXAMIC ACID