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(-) Description

Title :  SITE-DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN ENVIRONMENT IN PLEUROTUS ERYNGII VERSATILE PEROXIDASE
 
Authors :  F. J. Ruiz-Duenas, M. Morales, M. J. Mate, A. Romero, M. J. Martinez, A. S A. T. Martinez
Date :  18 Dec 07  (Deposition) - 29 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Lignin Peroxidase, Lignin Degradation, Manganese Peroxidase, Polyvalent Peroxidase, Aromatic-Substrate Binding, Mn-Independent Oxidation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. J. Ruiz-Duenas, M. Morales, M. J. Mate, A. Romero, M. J. Martinez, A. Smith, A. T. Martinez
Site-Directed Mutagenesis Of The Catalytic Tryptophan Environment In Pleurotus Eryngii Versatile Peroxidase
Biochemistry V. 47 1685 2008
PubMed-ID: 18201105  |  Reference-DOI: 10.1021/BI7020298

(-) Compounds

Molecule 1 - VERSATILE PEROXIDASE VPL2
    ChainsA
    EC Number1.11.1.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 31-347
    MutationYES
    Organism CommonTHISTLE MUSHROOM
    Organism ScientificPLEUROTUS ERYNGII
    Organism Taxid5323
    SynonymVERSATILE LIQUID PHASE PEROXIDASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:36 , HIS A:39 , GLU A:40 , LEU A:42 , THR A:45 , PHE A:46 , GLU A:140 , PRO A:141 , LEU A:165 , LEU A:166 , SER A:168 , HIS A:169 , ALA A:172 , ALA A:173 , ASP A:175 , LYS A:176 , VAL A:177 , PHE A:186 , LEU A:228 , SER A:230 , HOH A:2058 , HOH A:2071 , HOH A:2415 , HOH A:2416 , HOH A:2417BINDING SITE FOR RESIDUE HEM A1320
2AC2SOFTWAREHIS A:136 , GLU A:140 , ARG A:206 , HOH A:2207 , HOH A:2213 , HOH A:2411 , HOH A:2412 , HOH A:2413 , HOH A:2414BINDING SITE FOR RESIDUE SO4 A1318
3AC3SOFTWARESER A:170 , ASP A:187 , THR A:189 , VAL A:192 , ASP A:194BINDING SITE FOR RESIDUE CA A1319
4AC4SOFTWAREASP A:48 , GLY A:60 , ASP A:62 , SER A:64 , HOH A:2074 , HOH A:2103BINDING SITE FOR RESIDUE CA A1321
5AC5SOFTWARESER A:53 , THR A:55 , ARG A:151 , ASP A:154 , GLY A:297 , HOH A:2231 , HOH A:2418BINDING SITE FOR RESIDUE GOL A1322

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:15
2A:14 -A:278
3A:34 -A:114
4A:242 -A:307

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.VPL2_PLEER68-79  1A:38-49
2PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.VPL2_PLEER191-201  1A:161-171

(-) Exons   (0, 0)

(no "Exon" information available for 2VKA)

(-) 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 A from PDB  Type:PROTEIN  Length:317
 aligned with VPL2_PLEER | O94753 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:317
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       
           VPL2_PLEER    31 ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVWLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPALTA 347
               SCOP domains d2vkaa_ A: automated matches                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------peroxidase-2vkaA02 A:20-250                                                                                                                                                                                                            -DUF3415-2vkaA01 A:252-317                                          Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.........ee.........hhhhhhh...............ee........eehhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhee.hhhh................hhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------PEROXIDASE_-------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vka A   1 ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVWLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSFVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPALTA 317
                                    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       260       270       280       290       300       310       

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  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  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VPL2_PLEER | O94753)
molecular function
    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.
    GO:0052750    reactive-black-5:hydrogen-peroxide oxidoreductase activity    Catalysis of the reaction: reactive black 5 + hydrogen peroxide = oxidized reactive black 5 + 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:0042744    hydrogen peroxide catabolic process    The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
    GO:0046274    lignin catabolic process    The chemical reactions and pathways resulting in the breakdown of lignins, a class of polymers of phenylpropanoid units.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VPL2_PLEER | O947532boq 2w23 3fjw 3fkg 3fm1 3fm4 3fm6 3fmu 4fcn 4fcs 4fdq 4fef 4g05 5abn 5abo 5abq 5fnb 5fne

(-) Related Entries Specified in the PDB File

2boq CRYSTAL STRUCTURE OF VERSATILE PEROXIDASE