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(-) Description

Title :  DYE-DECOLORIZING PEROXIDASE (DYP) D171N
 
Authors :  Y. Sugano, T. Yoshida, H. Tsuge
Date :  19 Apr 10  (Deposition) - 27 Apr 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym./Biol. Unit :  A
Keywords :  Dyp, Dye-Decolorizing Peroxidase, Beta Barrel, Aspartic Acid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yoshida, H. Tsuge, H. Konno, T. Hisabori, Y. Sugano
The Catalytic Mechanism Of Dye-Decolorizing Peroxidase Dyp May Require The Swinging Movement Of An Aspartic Acid Residue
Febs J. V. 278 2387 2011
PubMed-ID: 21569205  |  Reference-DOI: 10.1111/J.1742-4658.2011.08161.X

(-) 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: RESIDUES IN UNP 57-498
    Gene: DYP
    Mutation: YES
    Organism Scientific: BJERKANDERA ADUSTA
    Organism Taxid: 5331
    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
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:165 , PHE A:169 , LEU A:170 , ASN A:171 , 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:1001 , HOH A:1030 , HOH A:1188 , HOH A:1201BINDING SITE FOR RESIDUE HEM A 501
2AC2SOFTWAREASN A:246 , HOH A:1076BINDING SITE FOR RESIDUE NAG A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MM1)

(-) 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 3MM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MM1)

(-) Exons   (0, 0)

(no "Exon" information available for 3MM1)

(-) 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:439
 aligned with Q8WZK8_9APHY | Q8WZK8 from UniProtKB/TrEMBL  Length:498

    Alignment length:439
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489         
         Q8WZK8_9APHY    60 TILPLNNIQGDILVGMKKQKERFVFFQVNDATSFKTALKTYVPERITSAAILISDPSQQPLAFVNLGFSNTGLQALGITDDLGDAQFPDGQFADAANLGDDLSQWVAPFTGTTIHGVFLIGSDQDDFLDQFTDDISSTFGSSITQVQALSGSARPGDQAGHEHFGFLDGISQPSVTGWETTVFPGQAVVPPGIILTGRDGDTGTRPSWALDGSFMAFRHFQQKVPEFNAYTLANAIPANSAGNLTQQEGAEFLGARMFGRWKSGAPIDLAPTADDPALGADPQRNNNFDYSDTLTDETRCPFGAHVRKTNPRQDLGGPVDTFHAMRSSIPYGPETSDAELASGVTAQDRGLLFVEYQSIIGNGFRFQQINWANNANFPFSKPITPGIEPIIGQTTPRTVGGLDPLNQNETFTVPLFVIPKGGEYFFLPSISALTATIAA 498
               SCOP domains d3mm1a_ A: Decolorizing peroxidase DyP                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhhh.hhhhh..eeeeeeehhhhhhhh.........hhhhhhhhhhhhhh.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
                 3mm1 A   4 TILPLNNIQGDILVGMKKQKERFVFFQVNDATSFKTALKTYVPERITSAAILISDPSQQPLAFVNLGFSNTGLQALGITDDLGDAQFPDGQFADAANLGDDLSQWVAPFTGTTIHGVFLIGSDQDDFLDQFTDDISSTFGSSITQVQALSGSARPGDQAGHEHFGFLNGISQPSVTGWETTVFPGQAVVPPGIILTGRDGDTGTRPSWALDGSFMAFRHFQQKVPEFNAYTLANAIPANSAGNLTQQEGAEFLGARMFGRWKSGAPIDLAPTADDPALGADPQRNNNFDYSDTLTDETRCPFGAHVRKTNPRQDLGGPVDTFHAMRSSIPYGPETSDAELASGVTAQDRGLLFVEYQSIIGNGFRFQQINWANNANFPFSKPITPGIEPIIGQTTPRTVGGLDPLNQNETFTVPLFVIPKGGEYFFLPSISALTATIAA 442
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433
   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 3MM1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MM1)

(-) 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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 Related Entries

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

(-) Related Entries Specified in the PDB File

3mm2 3mm3