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(-) Description

Title :  DYE-DECOLORIZING PEROXIDASE (DYP) COMPLEX WITH ASCORBIC ACID
 
Authors :  Y. Sugano, T. Yoshida, H. Tsuge
Date :  14 Sep 12  (Deposition) - 07 Nov 12  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Dyp, Dye-Decolorizing Peroxidase, Ascorbic Acid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Sugano, T. Yoshida, H. Tsuge
Dye-Decolorizing Peroxidase (Dyp) Complex With Ascorbic Aci
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DYP
    Chains: A
    EC Number: 1.11.1.19
    Engineered: YES
    Expression System: ASPERGILLUS ORYZAE
    Expression System Plasmid: PTAEX3
    Expression System Strain: M-2-3
    Expression System Taxid: 5062
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 57-498
    Gene: DYP
    Organism Scientific: BJERKANDERA ADUSTA
    Organism Taxid: 5331
    Strain: DEC 1
    Synonym: DYE-DECOLORIZING PEROXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ASC1Ligand/IonASCORBIC ACID
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:165 , PHE A:169 , LEU A:170 , GLY A:172 , ILE A:173 , SER A:174 , PHE A:223 , GLN A:225 , PHE A:261 , ARG A:263 , HIS A:308 , VAL A:309 , THR A:312 , ASN A:313 , ARG A:315 , ARG A:329 , LEU A:354 , PHE A:356 , GLU A:358 , PHE A:367 , GLN A:370 , HOH A:701 , HOH A:718 , HOH A:805 , HOH A:830BINDING SITE FOR RESIDUE HEM A 501
2AC2SOFTWAREGLY A:188 , ALA A:190 , ASN A:313 , ARG A:315 , GLY A:320 , PRO A:321 , HIS A:326 , HOH A:763 , HOH A:770 , HOH A:799 , HOH A:808BINDING SITE FOR RESIDUE ASC A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VXI)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:110 -Pro A:111
2Phe A:380 -Pro A:381
3Thr A:398 -Pro A:399

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VXI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VXI)

(-) Exons   (0, 0)

(no "Exon" information available for 3VXI)

(-) 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:438
 aligned with Q8WZK8_9APHY | Q8WZK8 from UniProtKB/TrEMBL  Length:498

    Alignment length:438
                                    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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490        
         Q8WZK8_9APHY    61 ILPLNNIQGDILVGMKKQKERFVFFQVNDATSFKTALKTYVPERITSAAILISDPSQQPLAFVNLGFSNTGLQALGITDDLGDAQFPDGQFADAANLGDDLSQWVAPFTGTTIHGVFLIGSDQDDFLDQFTDDISSTFGSSITQVQALSGSARPGDQAGHEHFGFLDGISQPSVTGWETTVFPGQAVVPPGIILTGRDGDTGTRPSWALDGSFMAFRHFQQKVPEFNAYTLANAIPANSAGNLTQQEGAEFLGARMFGRWKSGAPIDLAPTADDPALGADPQRNNNFDYSDTLTDETRCPFGAHVRKTNPRQDLGGPVDTFHAMRSSIPYGPETSDAELASGVTAQDRGLLFVEYQSIIGNGFRFQQINWANNANFPFSKPITPGIEPIIGQTTPRTVGGLDPLNQNETFTVPLFVIPKGGEYFFLPSISALTATIAA 498
               SCOP domains d3vxia_ A: Decolorizing peroxidase DyP                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhhh.hhhhh..eeeeeeehhhhhhhh..............hhhhhhhhh.hhhhh..........eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh..............ee............eehhhhh...........hhhhh..eeeeeeeeeehhhhhhhhhhhh...ee..ee.hhhhhhhhhhhhhhh...............hhhhhh.......................hhhhhhhhhhhhh........ee..eee....hhhhhhhh......eeeeeeee.hhhhhhhhhhhh...........................eee.........eee....eeeeeeeeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vxi A   5 ILPLNNIQGDILVGMKKQKERFVFFQVNDATSFKTALKTYVPERITSAAILISDPSQQPLAFVNLGFSNTGLQALGITDDLGDAQFPDGQFADAANLGDDLSQWVAPFTGTTIHGVFLIGSDQDDFLDQFTDDISSTFGSSITQVQALSGSARPGDQAGHEHFGFLDGISQPSVTGWETTVFPGQAVVPPGIILTGRDGDTGTRPSWALDGSFMAFRHFQQKVPEFNAYTLANAIPANSAGNLTQQEGAEFLGARMFGRWKSGAPIDLAPTADDPALGADPQRNNNFDYSDTLTDETRCPFGAHVRKTNPRQDLGGPVDTFHAMRSSIPYGPETSDAELASGVTAQDRGLLFVEYQSIIGNGFRFQQINWANNANFPFSKPITPGIEPIIGQTTPRTVGGLDPLNQNETFTVPLFVIPKGGEYFFLPSISALTATIAA 442
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VXI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VXI)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8WZK8_9APHY | Q8WZK8)
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: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.

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  3vxi
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  1.11.1.19
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 Related Entries

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

UniProtKB/TrEMBL
        Q8WZK8_9APHY | Q8WZK8: 2d3q 3afv 3mm1 3mm2 3mm3 3vxj

(-) Related Entries Specified in the PDB File

3vxj