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(-) Description

Title :  CRYSTAL STRUCTURE OF DITHINONITE REDUCED SOYBEAN ASCORBATE PEROXIDASE MUTANT W41A.
 
Authors :  C. L. Metcalfe, S. K. Badyal, E. L. Raven, P. C. E. Moody
Date :  08 Feb 08  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (2x)
Keywords :  Apx, Peroxidase, Heme Enzyme, Oxidoreductase, Dithionite Reduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Badyal, C. L. Metcalfe, J. Basran, I. Efimov, P. C. E. Moody, E. L. Raven
Iron Oxidation State Modulates Active Site Structure In A Heme Peroxidase.
Biochemistry V. 47 4403 2008
PubMed-ID: 18351739  |  Reference-DOI: 10.1021/BI702337N

(-) Compounds

Molecule 1 - ASCORBATE PEROXIDASE
    Chains: X
    EC Number: 1.11.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: SG13009
    Expression System Plasmid: SOYAPX/W41A
    Expression System Taxid: 562
    Expression System Vector: PQE30
    Fragment: RESIDUES 2-250
    Mutation: YES
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Other Details: FERROUS HEME WITH HIS42 IN THE OFF POSITION
    Synonym: CYTOSOLIC ASCORBATE PEROXIDASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : X
Biological Unit 1 (2x): X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO X:34 , ALA X:41 , PRO X:132 , ALA X:134 , LEU X:141 , PHE X:145 , LEU X:159 , SER X:160 , 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 , SER X:207 , TYR X:235 , HOH X:2236 , HOH X:2237 , HOH X:2238 , HOH X:2239 , HOH X:2240BINDING SITE FOR RESIDUE HEM X 251
2AC2SOFTWARETHR X:164 , THR X:180 , ASN X:182 , ILE X:185 , HOH X:2181BINDING SITE FOR RESIDUE NA X9252
3AC3SOFTWARESER X:43 , HOH X:2048 , HOH X:2063BINDING SITE FOR RESIDUE NA X9253

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VNZ)

(-) Sequences/Alignments

Asymmetric 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:248
 aligned with Q43758_SOYBN | Q43758 from UniProtKB/TrEMBL  Length:250

    Alignment length:248
                                    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 GKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFAD 249
               SCOP domains d2vnzx_ X: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains 2vnzX01 X:2-131,X:239-249  [code=1.10.520.10, no name defined]                                                                    2vnzX02 X:132-238 Peroxidase, domain 2                                                                     2vnzX01     CATH domains
               Pfam domains --------peroxidase-2vnzX01 X: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
                 2vnz X   2 GKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAAHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFAD 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
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (8, 8)

Asymmetric 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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  Q43758_SOYBN | Q43758
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  1.11.11.1
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 Related Entries

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

UniProtKB/TrEMBL
        Q43758_SOYBN | Q43758: 1oaf 1oag 1v0h 2cl4 2ggn 2ghc 2ghd 2ghe 2ghh 2ghk 2vcf 2vcn 2vcs 2vnx 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
2cl4 ASCORBATE PEROXIDASE R172A MUTANT
2ggn CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEMEPEROXIDASE
2ghc CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEMEPEROXIDASE
2ghd CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEMEPEROXIDASE
2ghe CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEMEPEROXIDASE
2ghh CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEMEPEROXIDASE
2ghk CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEMEPEROXIDASE
2vcf STRUCTURE OF ISONIAZID (INH) BOUND TO CYTOSOLIC SOYBEAN ASCORBATE PEROXIDASE
2vcn STRUCTURE OF ISONIAZID (INH) BOUND TO CYTOSOLIC SOYBEAN ASCORBATE PEROXIDASE MUTANT W41A
2vcs STRUCTURE OF ISONIAZID (INH) BOUND TO CYTOSOLIC SOYBEAN ASCORBATE PEROXIDASE MUTANT H42A
2vnx CRYSTAL STRUCTURE OF SOYBEAN ASCORBATE PEROXIDASE MUTANT W41A AFTER EXPOSURE TO A HIGH DOSE OF X-RAYS
2vo2 CRYSTAL STRUCTURE OF SOYBEAN ASCORBATE PEROXIDASE MUTANT W41A SUBJECTED TO LOW DOSE X-RAYS