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(-) Description

Title :  REACTION GEOMETRY AND THERMOSTABILITY MUTANT OF PYRANOSE 2-OXIDASE FROM THE WHITE-ROT FUNGUS PENIOPHORA SP.
 
Authors :  M. Bannwarth, S. Bastian, D. Heckmann-Pohl, F. Giffhorn, G. E. Schulz
Date :  28 Nov 05  (Deposition) - 13 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Flavoprotein, Rossmann-Fold, Phbh-Fold, Gmc Oxidoreductase, Glutathion-Reductase Related Fold, Tetramer, D2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bannwarth, D. Heckmann-Pohl, S. Bastian, F. Giffhorn, G. E. Schulz
Reaction Geometry And Thermostable Variant Of Pyranose 2-Oxidase From The White-Rot Fungus Peniophora Sp.
Biochemistry V. 45 6587 2006
PubMed-ID: 16716069  |  Reference-DOI: 10.1021/BI052465D

(-) Compounds

Molecule 1 - PYRANOSE 2-OXIDASE
    Chains: A
    EC Number: 1.1.3.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-24A-(+)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: P2OX, POXSG
    Organism Scientific: PENIOPHORA SP. SG
    Organism Taxid: 204723

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2KBG1Ligand/Ion2-KETO-BETA-D-GLUCOSE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2KBG4Ligand/Ion2-KETO-BETA-D-GLUCOSE
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
4PG44Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:169 , GLN A:448 , HIS A:450 , ASP A:452 , ARG A:472 , PHE A:474 , VAL A:546 , HIS A:548 , ASN A:593 , FAD A:1625 , HOH A:2075BINDING SITE FOR RESIDUE KBG A 1628
2AC2SOFTWAREVAL A:52 , GLY A:53 , GLY A:55 , PRO A:56 , ILE A:57 , ASP A:76 , ILE A:77 , ILE A:107 , THR A:158 , ARG A:159 , VAL A:160 , GLY A:163 , MET A:164 , HIS A:167 , TRP A:168 , THR A:169 , CYS A:170 , ALA A:171 , VAL A:281 , CYS A:283 , THR A:319 , ALA A:320 , HIS A:324 , LEU A:547 , ASN A:593 , THR A:595 , KBG A:1628 , HOH A:1640 , HOH A:1658 , HOH A:1659 , HOH A:1662 , HOH A:1673 , HOH A:1689 , HOH A:1690 , HOH A:1712 , HOH A:1729BINDING SITE FOR RESIDUE FAD A 1625
3AC3SOFTWARESER A:134 , PRO A:144 , GLU A:145 , GLN A:146 , ASP A:147 , PRO A:148 , HOH A:2229 , HOH A:2245 , HOH A:2312BINDING SITE FOR RESIDUE PG4 A 1626
4AC4SOFTWAREARG A:383 , THR A:390 , GLN A:611 , ASN A:612 , THR A:614 , HOH A:2311 , HOH A:2382BINDING SITE FOR RESIDUE PEG A 1627

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F5V)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:265 -Pro A:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F5V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F5V)

(-) Exons   (0, 0)

(no "Exon" information available for 2F5V)

(-) 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:577
 aligned with P2OX_PENSG | Q8J136 from UniProtKB/Swiss-Prot  Length:623

    Alignment length:577
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       
           P2OX_PENSG    43 MDIKYDVVIVGSGPIGCTYARELVGAGYKVAMFDIGEIDSGLKIGAHKKNTVEYQKNIDKFVNVIQGQLMSVSVPVNTLVVDTLSPTSWQASTFFVRNGSNPEQDPLRNLSGQAVTRVVGGMSTHWTCATPRFDREQRPLLVKDDADADDAEWDRLYTKAESYFQTGTDQFKESIRHNLVLNKLAEEYKGQRDFQQIPLAATRRSPTFVEWSSANTVFDLQNRPNTDAPEERFNLFPAVACERVVRNALNSEIESLHIHDLISGDRFEIKADVYVLTAGAVHNTQLLVNSGFGQLGRPNPTNPPELLPSLGSYITEQSLVFCQTVMSTELIDSVKSDMTIRGTPGELTYSVTYTPGASTNKHPDWWNEKVKNHMMQHQEDPLPIPFEDPEPQVTTLFQPSHPWHTQIHRDAFSYGAVQQSIDSRLIVDWRFFGRTEPKEENKLWFSDKITDAYNMPQPTFDFRFPAGRTSKEAEDMMTDMCVMSAKIGGFLPGSLPQFMEPGLVLHLGGTHRMGFDEKEDNCCVNTDSRVFGFKNLFLGGCGNIPTAYGANPTLTAMSLAIKSCEYIKQNFTPSPFT 619
               SCOP domains d2f5va1 A:43-354,A:553-619 Pyranose 2-oxidase                                                                                                                                                                                                                                                                           d2f5va2 A:355-552 Pyranose 2-oxidase                                                                                                                                                                  d2f5va1 A:43-354,A:553-619 Pyranose 2-oxidase                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhh..eeeee.................hhhhhhh..hhhhhhhhh.ee..........................................ee....hhhhhh........hhhhh......hhhhhhhhhhhhhhhhhhhhhee......hhhhhhhhhhhhhhh......ee..eeeeeee..eeee.hhhhhh....eee..eeeeeeeee..eeeeeeee......eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh............................eeeeeeeehhhhhhhhh...eee........eee..........hhhhhhhhhhhhhhh..............eee........eeeeee.............hhh.eeeeeeee........eeeeeeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhh..eee......ee.....................................eee.hhhhh.......hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f5v A  43 MDIKYDVVIVGSGPIGCTYARELVGAGYKVAMFDIGEIDSGLKIGAHKKNTVEYQKNIDKFVNVIQGQLMSVSVPVNTLVVDTLSPTSWQASTFFVRNGSNPEQDPLRNLSGQAVTRVVGGMSTHWTCATPRFDREQRPLLVKDDADADDAEWDRLYTKAESYFQTGTDQFKESIRHNLVLNKLAEEYKGQRDFQQIPLAATRRSPTFVEWSSANTVFDLQNRPNTDAPEERFNLFPAVACERVVRNALNSEIESLHIHDLISGDRFEIKADVYVLTAGAVHNTQLLVNSGFGQLGRPNPTNPPELLPSLGSYITEQSLVFCQTVMSTELIDSVKSDMTIRGTPGELTYSVTYTPGASTNKHPDWWNEKVKNHMMQHQEDPLPIPFEDPEPQVTTLFQPSHPWHTQIHRDAFSYGAVQQSIDSRLIVDWRFFGRTEPKEENKLWFSDKITDAYNMPQPTFDFRFPAGRTSKEAEDMMTDMCVMSAKIGGFLPGSLPQFMEPGLVLHLGGTHRMGFDEKEDNCCVNTDSRVFGFKNLFLGGCGNIPTAYGANPTLTAMSLAIKSCEYIKQNFTPSPFT 619
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F5V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F5V)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (P2OX_PENSG | Q8J136)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0050233    pyranose oxidase activity    Catalysis of the reaction: D-glucose + O(2) = 2-dehydro-D-glucose + H(2)O(2).
biological process
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        P2OX_PENSG | Q8J136: 1tzl 2f6c

(-) Related Entries Specified in the PDB File

1tzl 2f6c