Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  ASCORBATE PEROXIDASE R38K MUTANT
 
Authors :  C. L. Metcalfe, I. Efimov, A. Gumiero, E. L. Raven, P. C. E. Moody
Date :  20 Jan 11  (Deposition) - 12 Oct 11  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Heme Peroxidase, Peroxide Scavenger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Efimov, S. K. Badyal, C. L. Metcalfe, I. Macdonald, A. Gumiero, E. L. Raven, P. C. E. Moody
Proton Delivery To Ferryl Heme In A Heme Peroxidase: Enzymatic Use Of The Grotthuss Mechanism.
J. Am. Chem. Soc. V. 133 15376 2011
PubMed-ID: 21819069  |  Reference-DOI: 10.1021/JA2007017

(-) 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
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2-250
    Mutation: YES
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Synonym: CYTOSOLIC ASCORBATE PEROXIDASE 1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:34 , TRP A:41 , PRO A:132 , ALA A:134 , PHE A:145 , LEU A:159 , 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 , SER A:207 , TYR A:235 , HOH A:2083 , HOH A:2132 , HOH A:2133 , HOH A:2134BINDING SITE FOR RESIDUE HEM A 251
2AC2SOFTWAREPRO A:127 , ARG A:130 , HOH A:2135BINDING SITE FOR RESIDUE SO4 A 1251

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y6B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y6B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y6B)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y6B)

(-) 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 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 d2y6ba_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 2y6b A   2 GKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLKLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADA 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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y6B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y6B)

(-) Gene Ontology  (8, 8)

Asymmetric 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2y6b)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2y6b
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q43758_SOYBN | Q43758
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.11.1.11
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q43758_SOYBN | Q43758
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 2vnz 2vo2 2wd4 2xi6 2xif 2xih 2xj6 2y6a 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 HEME PEROXIDASE
2ghc CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEMEPEROXIDASE
2ghd CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEME PEROXIDASE
2ghe CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEME PEROXIDASE
2ghh CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEMEPEROXIDASE
2ghk CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEME PEROXIDASE
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
2vnz CRYSTAL STRUCTURE OF DITHINONITE REDUCED SOYBEAN ASCORBATE PEROXIDASE MUTANT W41A.
2vo2 CRYSTAL STRUCTURE OF SOYBEAN ASCORBATE PEROXIDASE MUTANT W41A SUBJECTED TO LOW DOSE X-RAYS
2wd4 ASCORBATE PEROXIDASE AS A HEME OXYGENASE: W41A VARIANT PRODUCT WITH T-BUTYL PEROXIDE
2xi6 THE NATURE OF THE FERRYL HEME SPECIES IN COMPOUNDS I AND II
2xj6 THE NATURE OF THE FERRYL HEME SPECIES IN COMPOUNDS I AND II
2y6a ASCORBATE PEROXIDASE R38A MUTANT