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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII. MUTANT VPI. MUTATED RESIDUES D69S, T70D, S86E, D146T, Q202L, H232E, Q239R AND S301K.
 
Authors :  F. J. Medrano, A. Romero
Date :  07 Aug 15  (Deposition) - 04 Nov 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A
Keywords :  Class Ii (Fungal) Peroxidases, Protoporphyrin Ix, Electron Transfer, Lignin Peroxidase, Lignin Degradation, Manganese Peroxidase, Mn-Independent Oxidation Phenolic Non-Phenolic Aromatics, Mnii Oxidation, Peroxidase, Polyvalent Peroxidase, Oxidoreductase, Heme, Hydrogen Peroxide, Iron, Manganese, Metal-Binding, Secreted, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Saez-Jimenez, E. Fernendez-Fueyo, F. J. Medrano, A. Romero, A. T. Martinez, F. J. Ruiz-Duenas
Improving The Ph-Stability Of Versatile Peroxidase By Comparative Structural Analysis With A Naturally-Stable Manganese Peroxidase.
Plos One V. 10 40984 2015
PubMed-ID: 26496708  |  Reference-DOI: 10.1371/JOURNAL.PONE.0140984

(-) Compounds

Molecule 1 - VERSATILE PEROXIDASE VPL2
    Chains: A
    EC Number: 1.11.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: W3110
    Expression System Taxid: 316407
    Mutation: YES
    Organism Common: BOLETUS OF THE STEPPES
    Organism Scientific: PLEUROTUS ERYNGII
    Organism Taxid: 5323
    Strain: IJFM, A169
    Synonym: VERSATILE PEROXIDASE, VERSATILE LIQUID PHASE PEROXIDASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:48 , GLY A:60 , ASP A:62 , SER A:64 , HOH A:2006 , HOH A:2009BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWARESER A:170 , ASP A:187 , THR A:189 , VAL A:192 , ASP A:194BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREHIS A:39 , GLU A:40 , LEU A:42 , ARG A:43 , PHE A:46 , GLU A:140 , PRO A:141 , SER A:168 , HIS A:169 , ALA A:172 , ALA A:173 , ALA A:174 , ASP A:175 , LYS A:176 , VAL A:177 , PHE A:186 , LEU A:228 , SER A:230 , MG A:1329BINDING SITE FOR RESIDUE HEM A 500
4AC4SOFTWAREASN A:96 , GLU A:140 , ASP A:143 , HOH A:2024 , HOH A:2026BINDING SITE FOR RESIDUE MG A1328
5AC5SOFTWAREGLU A:36 , GLU A:40 , ASP A:175 , HEM A:500BINDING SITE FOR RESIDUE MG A1329

(-) 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  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:2 -Cys A:3

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ABN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ABN)

(-) Exons   (0, 0)

(no "Exon" information available for 5ABN)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.ee...eee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.........ee.........hhhhhhh...............ee........eehhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhee.hhhh................hhhh......................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5abn A   2 TCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFSDIETNFPANAGIDEIVEAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVTSILARMGDAGFSPVEVVWLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETLLKGRLFPGTADNKGEAQSPLQGEIRLQSDELLARDPRTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLKDVEQACAATPFPALTADPGPVTSVPP 327
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 5ABN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ABN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ABN)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  5abn
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  VPL2_PLEER | O94753
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  1.11.1.16
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 Related Entries

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

UniProtKB/Swiss-Prot
        VPL2_PLEER | O94753: 2boq 2vka 2w23 3fjw 3fkg 3fm1 3fm4 3fm6 3fmu 4fcn 4fcs 4fdq 4fef 4g05 5abo 5abq 5fnb 5fne

(-) Related Entries Specified in the PDB File

5abo CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII. MUTANT VPI-BR. MUTATED RESIDUES T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K AND A314R.
5abq CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII. MUTANT VPI-SS. MUTATED RESIDUES T2K, A49C, A61C, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K AND A314R.