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(-) Description

Title :  ALDITOL OXIDASE FROM STREPTOMYCES COELICOLOR A3(2): COMPLEX WITH SULPHITE
 
Authors :  F. Forneris, A. Mattevi
Date :  05 Nov 07  (Deposition) - 08 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym./Biol. Unit :  A
Keywords :  Fad, Sugar, Polyol, Flavin, Oxidase, Flavoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forneris, D. P. H. M. Heuts, M. Delvecchio, S. Rovida, M. W. Fraaije, A. Mattevi
Structural Analysis Of The Catalytic Mechanism And Stereoselectivity In Streptomyces Coelicolor Alditol Oxidase.
Biochemistry V. 47 978 2008
PubMed-ID: 18154360  |  Reference-DOI: 10.1021/BI701886T

(-) Compounds

Molecule 1 - XYLITOL OXIDASE
    Chains: A
    EC Number: 1.1.3.41
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD/MYC-HISA
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 100226
    Strain: A3(2)
    Synonym: ALDITOL OXIDASE

 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
1CL1Ligand/IonCHLORIDE ION
2SFD1Ligand/Ion(S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHOXY)(HYDROXY)PHOSPHORYLOXY)(HYDROXY)PHOSPHORYLOXY)-2,3,4-TRIHYDROXYPENTYL)-7,8-DIMETHYL-2,4-DIOXO-2,3,4,4A-TETRAHYDROBENZO[G]PTERIDINE-5(10H)-SULFONICACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:9 , ARG A:40 , VAL A:41 , LEU A:42 , GLY A:43 , SER A:44 , GLY A:45 , HIS A:46 , SER A:47 , ILE A:51 , LEU A:63 , ALA A:105 , SER A:106 , ILE A:110 , SER A:111 , ALA A:113 , GLY A:114 , SER A:115 , ALA A:117 , THR A:118 , THR A:120 , HIS A:121 , GLY A:164 , GLY A:167 , VAL A:169 , GLN A:288 , ARG A:322 , HIS A:343 , HIS A:372 , GLY A:374 , LYS A:375 , HOH A:2424 , HOH A:2523 , HOH A:2524 , HOH A:2525BINDING SITE FOR RESIDUE SFD A1418
2AC2SOFTWARELEU A:192 , ALA A:193 , PRO A:219 , HOH A:2177BINDING SITE FOR RESIDUE CL A1419

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VFV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_PCMHPS51387 PCMH-type FAD-binding domain profile.XYOA_STRCO13-179  1A:13-179

(-) Exons   (0, 0)

(no "Exon" information available for 2VFV)

(-) 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:418
 aligned with XYOA_STRCO | Q9ZBU1 from UniProtKB/Swiss-Prot  Length:418

    Alignment length:418
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        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        
           XYOA_STRCO     - -MSDITVTNWAGNITYTAKELLRPHSLDALRALVADSARVRVLGSGHSFNEIAEPGDGGVLLSLAGLPSVVDVDTAARTVRVGGGVRYAELARVVHARGLALPNMASLPHISVAGSVATGTHGSGVGNGSLASVVREVELVTADGSTVVIARGDERFGGAVTSLGALGVVTSLTLDLEPAYEMEQHVFTELPLAGLDPATFETVMAAAYSVSLFTDWRAPGFRQVWLKRRTDRPLDGFPYAAPAAEKMHPVPGMPAVNCTEQFGVPGPWHERLPHFRAEFTPSSGAELQSEYLMPREHALAALHAMDAIRETLAPVLQTCEIRTVAADAQWLSPAYGRDTVAAHFTWVEDTAAVLPVVRRLEEALVPFAARPHWGKVFTVPAGELRALYPRLADFGALAGALDPAGKFTNAFVRGVLA 417
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhh..eeee................eeee.......eeee....eeeee...hhhhhhhhhhhh.ee..........hhhhhhhh..........hhhh.eeeeeee.....eeeee....hhhhh........eeeeeeee.ee..eeeeeeeeee.....hhhhhhhhhh...eeeeee......eeeeeeeee...........ee...........hhhh........ee.hhh...............eeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeee..............eeeeeeee..hhhhhhhhhhhhhhhhhhhh.ee........hhhhhhh...hhhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------FAD_PCMH  PDB: A:13-179 UniProt: 13-179                                                                                                                                ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vfv A   0 FMSDITVTNWAGNITYTAKELLRPHSLDALRALVADSARVRVLGSGHSFNEIAEPGDGGVLLSLAGLPSVVDVDTAARTVRVGGGVRYAELARVVHARGLALPNMASLPHISVAGSVATGTHGSGVGNGSLASVVREVELVTADGSTVVIARGDERFGGAVTSLGALGVVTSLTLDLEPAYEMEQHVFTELPLAGLDPATFETVMAAAYSVSLFTDWRAPGFRQVWLKRRTDRPLDGFPYAAPAAEKMHPVPGMPAVNCTEQFGVPGPWHERLPHFRAEFTPSSGAELQSEYLMPREHALAALHAMDAIRETLAPVLQTCEIRTVAADAQWLSPAYGRDTVAAHFTWVEDTAAVLPVVRRLEEALVPFAARPHWGKVFTVPAGELRALYPRLADFGALAGALDPAGKFTNAFVRGVLA 417
                                     9        19        29        39        49        59        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
   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  (0, 0)

(no "SCOP Domain" information available for 2VFV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYOA_STRCO | Q9ZBU1)
molecular function
    GO:0003885    D-arabinono-1,4-lactone oxidase activity    Catalysis of the reaction: D-arabinono-1,4-lactone + O(2) = dehydro-D-arabinono-1,4-lactone + H(2)O(2) + H(+).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0050582    xylitol oxidase activity    Catalysis of the reaction: xylitol + O2 = xylose + H2O2.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  2vfv
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  XYOA_STRCO | Q9ZBU1
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  1.1.3.41
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYOA_STRCO | Q9ZBU1: 2vfr 2vfs 2vft 2vfu

(-) Related Entries Specified in the PDB File

2vfr ALDITOL OXIDASE FROM STREPTOMYCES COELICOLOR A3(2): NATIVE ENZYME
2vfs ALDITOL OXIDASE FROM STREPTOMYCES COELICOLOR A3(2): COMPLEX WITH XYLITOL
2vft ALDITOL OXIDASE FROM STREPTOMYCES COELICOLOR A3(2): COMPLEX WITH SORBITOL
2vfu ALDITOL OXIDASE FROM STREPTOMYCES COELICOLOR A3(2): COMPLEX WITH MANNITOL