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(-) Description

Title :  CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM II
 
Authors :  F. J. Medrano, A. Romero
Date :  05 May 13  (Deposition) - 15 Jan 14  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.39
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Class Ii (Fungal) Peroxidases, Protoporphyrin Ix, Electron T Lignin Peroxidase, Lignin Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Fernandez-Fueyo, F. J. Ruiz-Duenas, M. J. Martinez, A. Romero, K. E. Hammel, F. J. Medrano, A. T. Martinez
Ligninolytic Peroxidase Genes In The Oyster Mushroom Genome: Heterologous Expression, Molecular Structure, Catalytic And Stability Properties, And Lignin-Degrading Ability.
Biotechnol. Biofuels V. 7 2 2014
PubMed-ID: 24387130  |  Reference-DOI: 10.1186/1754-6834-7-2

(-) Compounds

Molecule 1 - MANGANESE PEROXIDASE 4
    Chains: A
    EC Number: 1.11.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: K-12
    Expression System Taxid: 316407
    Expression System Variant: W3110
    Organism Common: OYSTER MUSHROOM
    Organism Scientific: PLEUROTUS OSTREATUS
    Organism Taxid: 5322

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:49 , GLY A:67 , ASP A:69 , SER A:71 , HOH A:2093 , HOH A:2099BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWARESER A:177 , ASP A:194 , THR A:196 , ASP A:199 , ASP A:201BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREHIS A:40 , ARG A:44 , PHE A:47 , GLU A:147 , PRO A:148 , LEU A:172 , LEU A:173 , SER A:175 , HIS A:176 , ALA A:179 , ALA A:180 , GLN A:181 , ASP A:182 , THR A:183 , ILE A:184 , PHE A:193 , LEU A:235 , SER A:237 , MET A:269 , HOH A:2077 , HOH A:2086BINDING SITE FOR RESIDUE HEM A 500
4AC4SOFTWAREASN A:12 , ILE A:283 , ASP A:284 , HOH A:2026 , HOH A:2399BINDING SITE FOR RESIDUE SO4 A1339
5AC5SOFTWAREASP A:185 , LYS A:187 , ASP A:218 , SER A:219 , HIS A:221 , HOH A:2289 , HOH A:2329BINDING SITE FOR RESIDUE SO4 A1340
6AC6SOFTWAREASP A:325 , LYS A:326 , HOH A:2459 , HOH A:2480BINDING SITE FOR RESIDUE SO4 A1341
7AC7SOFTWARELYS A:101 , LYS A:316 , THR A:328BINDING SITE FOR RESIDUE SO4 A1342

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:16
2A:15 -A:285
3A:35 -A:121
4A:249 -A:314

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BM2)

(-) Exons   (0, 0)

(no "Exon" information available for 4BM2)

(-) 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:337
 aligned with W5IDB6_PLEOS | W5IDB6 from UniProtKB/TrEMBL  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
         W5IDB6_PLEOS     2 AKCSKGRTASNDACCVWFDVLDDIQENLFDGGECGEEVHESLRLTFHDAIGFSPALTRQGKFGGGGADGSIMLFSDIETNFAANNGVDDIVEQQKPIAIKHQVSFGDFIQFAGAVGSSNCAGGPRIQFLAGRSNVTKPSPDHLVPEPFDSVTSILARMGDAGFKPDEVVALLASHSVAAQDTIDPKLAGHPFDSTPSDFDSQFFVETLLKGTLIPGDSLHKGQVKSPLPGEFRLQSDELLARDSRTSCEWQSFISNPNSMVPKFERAMAKMATLGQNPKKLIDCSEVIPVPRGRVKQPTLPAGKTIKDIEASCRKAPFPRLPTDKGTFTSILPVPSS 338
               SCOP domains d4bm2a_ A: automated matches                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhh.........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhh............hhhhhhh...............ee........eehhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhee.hhhh................hhhh............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bm2 A   2 AKCSKGRTASNDACCVWFDVLDDIQENLFDGGECGEEVHESLRLTFHDAIGFSPALTRQGKFGGGGADGSIMLFSDIETNFAANNGVDDIVEQQKPIAIKHQVSFGDFIQFAGAVGSSNCAGGPRIQFLAGRSNVTKPSPDHLVPEPFDSVTSILARMGDAGFKPDEVVALLASHSVAAQDTIDPKLAGHPFDSTPSDFDSQFFVETLLKGTLIPGDSLHKGQVKSPLPGEFRLQSDELLARDSRTSCEWQSFISNPNSMVPKFERAMAKMATLGQNPKKLIDCSEVIPVPRGRVKQPTLPAGKTIKDIEASCRKAPFPRLPTDKGTFTSILPVPSS 338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "CATH Domain" information available for 4BM2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BM2)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (W5IDB6_PLEOS | W5IDB6)
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.
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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  1.11.1.13
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 Related Entries

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

UniProtKB/TrEMBL
        W5IDB6_PLEOS | W5IDB6: 4bm1 4bm3 4bm4

(-) Related Entries Specified in the PDB File

4blk CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM I
4bll CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM II
4bln CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM III
4blx CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM IV
4bly CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM V
4blz CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM VI
4bm0 CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM VII
4bm1 CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM I
4bm3 CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM III
4bm4 CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM IV