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(-) Description

Title :  STRUCTURE OF ISONIAZID (INH) BOUND TO CYTOSOLIC SOYBEAN ASCORBATE PEROXIDASE
 
Authors :  C. L. Metcalfe, I. K. Macdonald, K. A. Brown, E. L. Raven, P. C. E. Moody
Date :  21 Sep 07  (Deposition) - 04 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  X
Keywords :  Cytochrome C Peroxidase, Ccp, Inh, Isoniazid, Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Metcalfe, I. K. Macdonald, E. J. Murphy, K. A. Brown, E. L. Raven, P. C. E. Moody
The Tuberculosis Prodrug Isoniazid Bound To Activating Peroxidases.
J. Biol. Chem. V. 283 6193 2008
PubMed-ID: 18056997  |  Reference-DOI: 10.1074/JBC.M707412200

(-) Compounds

Molecule 1 - ASCORBATE PEROXIDASE FROM SOYBEAN CYTOSOL
    Chains: X
    EC Number: 1.11.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SAPX4
    Expression System Strain: SG13009
    Expression System Taxid: 562
    Fragment: RESIDUES 2-250
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847

 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
2ISZ2Ligand/Ion4-(DIAZENYLCARBONYL)PYRIDINE
3NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG X:38 , HIS X:42 , SER X:69 , ALA X:70 , ASN X:72 , PRO X:132 , ALA X:134 , ARG X:172 , SER X:173 , HEM X:1254 , HOH X:2237 , HOH X:2377 , HOH X:2378BINDING SITE FOR RESIDUE ISZ X1252
2AC2SOFTWARELYS X:30 , CYS X:32 , LEU X:35 , ILE X:76 , ARG X:172 , HOH X:2380 , HOH X:2381BINDING SITE FOR RESIDUE ISZ X1253
3AC3SOFTWAREPRO 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 , ISZ X:1252 , HOH X:2084 , HOH X:2277 , HOH X:2381 , HOH X:2382 , HOH X:2383BINDING SITE FOR RESIDUE HEM X1254
4AC4SOFTWARETHR X:164 , THR X:180 , ASN X:182 , ILE X:185 , ASP X:187 , HOH X:2295BINDING SITE FOR RESIDUE NA X1255

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp X:249 -Ala X:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VCF)

(-) 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:251
 aligned with Q43758_SOYBN | Q43758 from UniProtKB/TrEMBL  Length:250

    Alignment length:251
                                                                                                                                                                                                                                                                                   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-   -
               SCOP domains d2vcfx_ X: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 2vcfX01 X:1-131,X:239-251  [code=1.10.520.10, no name defined]                                                                     2vcfX02 X:132-238 Peroxidase, domain 2                                                                     2vcfX01       CATH domains
               Pfam domains ---------peroxidase-2vcfX01 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
                 2vcf X   1 SGKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADAH 251
                                    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
(-)
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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  Cis Peptide Bonds
    Asp X:249 - Ala X:250   [ RasMol ]  
 

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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 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
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