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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII
 
Authors :  K. Piontek, A. T. Martinez, T. Choinowski, D. A. Plattner
Date :  15 Dec 08  (Deposition) - 15 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Class Ii (Fungal) Peroxidases, Protoporphyrin Ix, Glycoprotein Electron Transfer, Lignin Peroxidase, Lignin Degradation, Manganese Peroxidase, Mn-Independent Oxidation Phenolic Non-Phenolic Aromatics, Mnii Oxidation, Peroxidase, Polyvalent Peroxidase, Oxidoreductase, Heme, Glycoprotein, Hydrogen Peroxide, Iron, Manganese, Metal-Binding, Secreted, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Piontek, T. Choinowski, M. Perez-Boada, F. J. Ruiz-Duenas, M. J. Martinez, D. A. Plattner, A. T. Martinez
Structural And Site-Directed Mutagenesis Study Of Versatile Peroxidase Oxidizing Both Mn(Ii) And Aromatic Substrates
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - VERSATILE PEROXIDASE VPL2
    ChainsA, B
    EC Number1.11.1.16
    Organism CommonBOLETUS OF THE STEPPES
    Organism ScientificPLEUROTUS ERYNGII
    Organism Taxid5323
    StrainIJFM A169
    SynonymVERSATILE LIQUID PHASE PEROXIDASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 20)

Asymmetric Unit (6, 20)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA4Ligand/IonCALCIUM ION
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MAN8Ligand/IonALPHA-D-MANNOSE
5MN2Ligand/IonMANGANESE (II) ION
6NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MAN4Ligand/IonALPHA-D-MANNOSE
5MN-1Ligand/IonMANGANESE (II) ION
6NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MAN4Ligand/IonALPHA-D-MANNOSE
5MN-1Ligand/IonMANGANESE (II) ION
6NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:36 , HIS A:39 , GLU A:40 , LEU A:42 , ARG A:43 , THR A:45 , PHE A:46 , GLU A:140 , PRO A:141 , LEU A:165 , 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 , MN A:353 , HOH A:400 , HOH A:451 , HOH A:482BINDING SITE FOR RESIDUE HEM A 350
02AC2SOFTWAREASP A:48 , GLY A:60 , ASP A:62 , SER A:64 , HOH A:415 , HOH A:507BINDING SITE FOR RESIDUE CA A 351
03AC3SOFTWARESER A:170 , ASP A:187 , THR A:189 , VAL A:192 , ASP A:194BINDING SITE FOR RESIDUE CA A 352
04AC4SOFTWAREGLU A:36 , GLU A:40 , ASP A:175 , HEM A:350 , HOH A:451 , HOH A:482BINDING SITE FOR RESIDUE MN A 353
05AC5SOFTWAREASN A:96 , HOH A:372 , HOH A:437 , HOH A:462 , HOH A:480 , HOH A:517BINDING SITE FOR RESIDUE NAG A 361
06AC6SOFTWARECYS A:242 , GLN A:245 , SER A:246 , ALA A:309 , THR A:310 , HOH A:562BINDING SITE FOR RESIDUE MAN A 371
07AC7SOFTWAREGLN A:223 , SER A:324 , VAL A:325 , HOH A:345 , HOH A:503BINDING SITE FOR RESIDUE MAN A 381
08AC8SOFTWARESER A:188 , PRO A:295 , ALA A:296 , ASP A:318 , THR A:323 , MAN A:392 , HOH A:478BINDING SITE FOR RESIDUE BMA A 391
09AC9SOFTWARESER A:188 , SER A:324 , PRO A:326 , HOH A:358 , BMA A:391 , HOH A:550BINDING SITE FOR RESIDUE MAN A 392
10BC1SOFTWAREARG A:119 , THR A:284 , HOH A:509 , HOH A:530 , ALA B:67 , PHE B:68 , THR B:70 , ILE B:71BINDING SITE FOR RESIDUE MAN A 401
11BC2SOFTWAREGLU B:36 , HIS B:39 , GLU B:40 , LEU B:42 , ARG B:43 , PHE B:46 , GLU B:140 , PRO B:141 , SER B:168 , HIS B:169 , ALA B:172 , ALA B:173 , ALA B:174 , ASP B:175 , LYS B:176 , VAL B:177 , SER B:230 , HOH B:338 , HOH B:346 , MN B:353 , HOH B:485 , HOH B:489BINDING SITE FOR RESIDUE HEM B 350
12BC3SOFTWAREASP B:48 , GLY B:60 , ASP B:62 , SER B:64 , HOH B:365 , HOH B:425BINDING SITE FOR RESIDUE CA B 351
13BC4SOFTWARESER B:170 , ASP B:187 , THR B:189 , VAL B:192 , ASP B:194BINDING SITE FOR RESIDUE CA B 352
14BC5SOFTWAREGLU B:36 , GLU B:40 , ASP B:175 , HOH B:338 , HOH B:346 , HEM B:350BINDING SITE FOR RESIDUE MN B 353
15BC6SOFTWAREASN B:96BINDING SITE FOR RESIDUE NAG B 361
16BC7SOFTWARECYS B:242 , GLN B:245 , SER B:246 , CYS B:307 , ALA B:309 , THR B:310BINDING SITE FOR RESIDUE MAN B 371
17BC8SOFTWAREGLU A:26 , ASN A:27 , SER B:324BINDING SITE FOR RESIDUE MAN B 381
18BC9SOFTWAREPRO B:295 , ALA B:296 , ASP B:318 , THR B:323 , MAN B:392 , HOH B:510BINDING SITE FOR RESIDUE BMA B 391
19CC1SOFTWAREGLU A:26 , ASN A:27 , SER B:188 , SER B:324 , PRO B:326 , BMA B:391 , HOH B:496BINDING SITE FOR RESIDUE MAN B 392
20CC2SOFTWAREALA A:67 , THR A:70 , THR B:284 , HOH B:438 , HOH B:502BINDING SITE FOR RESIDUE MAN B 401

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:3 -A:15
2A:14 -A:278
3A:34 -A:114
4A:242 -A:307
5B:3 -B:15
6B:14 -B:278
7B:34 -B:114
8B:242 -B:307

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FJW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.VPL2_PLEER68-79
 
  2A:38-49
B:38-49
2PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.VPL2_PLEER191-201
 
  2A:161-171
B:161-171
Biological Unit 1 (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
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.VPL2_PLEER68-79
 
  1-
B:38-49
2PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.VPL2_PLEER191-201
 
  1-
B:161-171

(-) Exons   (0, 0)

(no "Exon" information available for 3FJW)

(-) Sequences/Alignments

Asymmetric 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:331
 aligned with VPL2_PLEER | O94753 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:331
                                    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       350       360 
           VPL2_PLEER    31 ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVWLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPALTADPGPVTSVPPVPGS 361
               SCOP domains d3fjwa_ A: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.........ee.........hhhhhhh...............ee........eehhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhee.....................hhhhh............................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------PEROXIDASE_---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fjw A   1 ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVWLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPALTADPGPVTSVPPVPGS 331
                                    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       320       330 

Chain B from PDB  Type:PROTEIN  Length:331
 aligned with VPL2_PLEER | O94753 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:331
                                    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       350       360 
           VPL2_PLEER    31 ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVWLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPALTADPGPVTSVPPVPGS 361
               SCOP domains d3fjwb_ B: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.........ee.........hhhhhhh...............ee........eehhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhee.hhhh................hhhhh............................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------PEROXIDASE_---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fjw B   1 ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVWLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPALTADPGPVTSVPPVPGS 331
                                    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       320       330 

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 2vka 2w23 3fkg 3fm1 3fm4 3fm6 3fmu 4fcn 4fcs 4fdq 4fef 4g05 5abn 5abo 5abq 5fnb 5fne

(-) Related Entries Specified in the PDB File

2boq RECOMBINANTE VERSATILE PEROXIDASE WILD TYPE INCUBATED WITH H2O2
3fkg RECOMBINANTE VERSATILE PEROXIDASE Q33N, G191E VARIANT
3fm1 RECOMBINANTE VERSATILE PEROXIDASE G191Q VARIANT, CRYSTALS SOAKED WITH MN2+
3fm4 RECOMBINANTE VERSATILE PEROXIDASE D175A VARIANT
3fm6 RECOMBINANTE VERSATILE PEROXIDASE F142Q VARIANT
3fmu RECOMBINANTE VERSATILE PEROXIDASE W164S VARIANT