Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE QUERCETIN 2,3-DIOXYGENASE (YXAG, BSU39980) FROM BACILLUS SUBTILIS AT 2.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  15 May 06  (Deposition) - 30 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Double-Stranded Beta-Helix, Bicupin, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of (2636545) From Bacillus Subtilis At 2. 60 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - QUERCETIN 2,3-DIOXYGENASE
    Chains: A, B
    EC Number: 1.13.11.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: QDOI
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: QUERCETINASE, FLAVONOL 2,4-DIOXYGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 42)

Asymmetric/Biological Unit (5, 42)
No.NameCountTypeFull Name
1EDO18Ligand/Ion1,2-ETHANEDIOL
2FE4Ligand/IonFE (III) ION
3MSE16Mod. Amino AcidSELENOMETHIONINE
4TLA2Ligand/IonL(+)-TARTARIC ACID
5TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:62 , HIS A:64 , GLU A:69 , HIS A:103 , EDO A:502BINDING SITE FOR RESIDUE FE A 500
02AC2SOFTWAREHIS A:234 , HIS A:236 , GLU A:241 , HIS A:275 , TLA A:503BINDING SITE FOR RESIDUE FE A 501
03AC3SOFTWAREHIS B:62 , HIS B:64 , GLU B:69 , HIS B:103 , EDO B:502BINDING SITE FOR RESIDUE FE B 500
04AC4SOFTWAREHIS B:234 , HIS B:236 , GLU B:241 , HIS B:275 , TLA B:503BINDING SITE FOR RESIDUE FE B 501
05AC5SOFTWAREHIS A:62 , HIS A:64 , GLU A:69 , HIS A:103 , TYR A:127 , FE A:500BINDING SITE FOR RESIDUE EDO A 502
06AC6SOFTWAREHIS A:234 , HIS A:236 , GLU A:241 , HIS A:275 , TYR A:277 , PRO A:297 , PHE A:298 , PHE A:299 , FE A:501BINDING SITE FOR RESIDUE TLA A 503
07AC7SOFTWAREHIS B:62 , HIS B:64 , GLU B:69 , HIS B:103 , TYR B:127 , FE B:500BINDING SITE FOR RESIDUE EDO B 502
08AC8SOFTWAREHIS B:234 , HIS B:236 , GLU B:241 , PHE B:243 , HIS B:275 , TYR B:277 , PRO B:297 , PHE B:298 , PHE B:299 , FE B:501 , HOH B:648BINDING SITE FOR RESIDUE TLA B 503
09AC9SOFTWAREGLU A:307 , HIS A:309 , ARG B:30 , LYS B:55 , PRO B:141 , TYR B:142BINDING SITE FOR RESIDUE TRS B 504
10BC1SOFTWAREARG A:30 , LYS A:55 , PRO A:141 , TYR A:142 , HIS B:309 , HOH B:600BINDING SITE FOR RESIDUE TRS A 504
11BC2SOFTWARELEU A:27 , GLY A:29 , ILE A:130 , ASN A:132 , GLU A:145 , ARG A:151 , HOH A:620BINDING SITE FOR RESIDUE EDO A 505
12BC3SOFTWARESER A:91 , EDO A:510 , HOH A:529 , GLY B:76 , ILE B:90 , SER B:91BINDING SITE FOR RESIDUE EDO B 505
13BC4SOFTWARELEU B:27 , ILE B:130 , ASN B:132 , GLU B:145 , HOH B:592 , HOH B:604BINDING SITE FOR RESIDUE EDO B 506
14BC5SOFTWAREGLY B:195 , ARG B:197 , TYR B:306BINDING SITE FOR RESIDUE EDO B 507
15BC6SOFTWAREEDO A:507 , LEU B:74 , ARG B:113 , TYR B:244 , GLY B:264BINDING SITE FOR RESIDUE EDO B 508
16BC7SOFTWAREGLU A:247 , TYR A:283 , LYS A:285 , HOH A:573 , ASP B:75 , ARG B:111 , HOH B:571BINDING SITE FOR RESIDUE EDO A 506
17BC8SOFTWAREGLU B:79 , THR B:81 , ARG B:86 , SER B:104 , TYR B:105 , ARG B:106BINDING SITE FOR RESIDUE EDO B 509
18BC9SOFTWAREGLU A:247 , HOH A:544 , HOH A:560 , ARG B:111 , PRO B:263 , EDO B:508BINDING SITE FOR RESIDUE EDO A 507
19CC1SOFTWAREALA A:173 , LEU A:175 , ALA B:173BINDING SITE FOR RESIDUE EDO B 510
20CC2SOFTWARELYS A:55 , LYS A:77 , ALA B:176 , GLU B:191 , HOH B:623BINDING SITE FOR RESIDUE EDO A 508
21CC3SOFTWAREHIS A:282 , HOH A:590 , GLY B:21 , ARG B:25BINDING SITE FOR RESIDUE EDO A 509
22CC4SOFTWARESER A:20 , ARG A:111 , ARG A:113 , PRO A:263 , GLU B:247 , HOH B:527 , HOH B:564BINDING SITE FOR RESIDUE EDO B 511
23CC5SOFTWARELEU A:175 , LYS B:55 , LYS B:77 , GLN B:108BINDING SITE FOR RESIDUE EDO B 512
24CC6SOFTWAREGLY A:76 , ILE A:90 , SER A:91 , SER B:91 , EDO B:505BINDING SITE FOR RESIDUE EDO A 510
25CC7SOFTWAREASP B:196 , LYS B:212 , ARG B:300BINDING SITE FOR RESIDUE EDO B 513
26CC8SOFTWARELEU A:74 , ARG A:113 , TYR A:244 , GLY A:264BINDING SITE FOR RESIDUE EDO A 511

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H0V)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:291 -Pro A:292
2Lys A:336 -Pro A:337
3Val B:291 -Pro B:292
4Lys B:336 -Pro B:337

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H0V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H0V)

(-) Exons   (0, 0)

(no "Exon" information available for 2H0V)

(-) 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:335
 aligned with QDOI_BACSU | P42106 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:335
                                    12        22        32        42        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     
           QDOI_BACSU     3 TLCTHSLPKEKMPYLLRSGEGERYLFGRQVATVMANGRSTGDLFEIVLLSGGKGDAFPLHVHKDTHEGILVLDGKLELTLDGERYLLISGDYANIPAGTPHSYRMQSHRTRLVSYTMKGNVAHLYSVIGNPYDHAEHPPYASEEVSNERFAEAAAVADIVFLDEAKPACSAKLAELTELPDGAVPYVLESGEGDRLLTGDQLHRIVAAQKNTDGQFIVVSSEGPKGDRIVDHYHEYHTETFYCLEGQMTMWTDGQEIQLNPGDFLHVPANTVHSYRLDSHYTKMVGVLVPGLFEPFFRTLGDPYEGHIFPCEPQALRFDRILQNIEALDLKVMKP 337
               SCOP domains d2h0va_ A: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee.....eeeee..eeeeeeehhhhhh..eeeeeeee....eeeeee.....eeeeeee..eeeee..eeeee....eeee.....eeeee....eeeeeeee.....hhhhhhhee..............hhhhhhhhhh....ee..........ee............eee.....eeeee..eeeeeeehhhhh....eeeeeee..............eeeeeeee..eeeee..eeeee....eeee.....eeeee....eeeeeeee.....hhhhhhhee..............hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h0v A   3 TLCTHSLPKEKmPYLLRSGEGERYLFGRQVATVmANGRSTGDLFEIVLLSGGKGDAFPLHVHKDTHEGILVLDGKLELTLDGERYLLISGDYANIPAGTPHSYRmQSHRTRLVSYTmKGNVAHLYSVIGNPYDHAEHPPYASEEVSNERFAEAAAVADIVFLDEAKPACSAKLAELTELPDGAVPYVLESGEGDRLLTGDQLHRIVAAQKNTDGQFIVVSSEGPKGDRIVDHYHEYHTETFYCLEGQmTmWTDGQEIQLNPGDFLHVPANTVHSYRLDSHYTKmVGVLVPGLFEPFFRTLGDPYEGHIFPCEPQALRFDRILQNIEALDLKVmKP 337
                                    12 |      22        32   |    42        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  |  
                                      14-MSE                36-MSE                                                                107-MSE     119-MSE                                                                                                                            250-MSE                             286-MSE                                          335-MSE
                                                                                                                                                                                                                                                                                   252-MSE                                                                                 


Chain B from PDB  Type:PROTEIN  Length:335
 aligned with QDOI_BACSU | P42106 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:335
                                    12        22        32        42        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     
           QDOI_BACSU     3 TLCTHSLPKEKMPYLLRSGEGERYLFGRQVATVMANGRSTGDLFEIVLLSGGKGDAFPLHVHKDTHEGILVLDGKLELTLDGERYLLISGDYANIPAGTPHSYRMQSHRTRLVSYTMKGNVAHLYSVIGNPYDHAEHPPYASEEVSNERFAEAAAVADIVFLDEAKPACSAKLAELTELPDGAVPYVLESGEGDRLLTGDQLHRIVAAQKNTDGQFIVVSSEGPKGDRIVDHYHEYHTETFYCLEGQMTMWTDGQEIQLNPGDFLHVPANTVHSYRLDSHYTKMVGVLVPGLFEPFFRTLGDPYEGHIFPCEPQALRFDRILQNIEALDLKVMKP 337
               SCOP domains d2h0vb_ B: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee.....eeeee..eeeeeeehhhhhh..eeeeeeee....eeeeee.....eeeeeee..eeeee..eeeee....eeee.....eeeee....eeeeeeee...hhhhhhhhhee..............hhhhhhhhhhhh..ee..........ee............eee.....eeeee..eeeeeeehhhhh....eeeeeee..............eeeeeeee..eeeee..eeeee....eeee.....eeeee....eeeeeeee.....hhhhhhhee..............hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h0v B   3 TLCTHSLPKEKmPYLLRSGEGERYLFGRQVATVmANGRSTGDLFEIVLLSGGKGDAFPLHVHKDTHEGILVLDGKLELTLDGERYLLISGDYANIPAGTPHSYRmQSHRTRLVSYTmKGNVAHLYSVIGNPYDHAEHPPYASEEVSNERFAEAAAVADIVFLDEAKPACSAKLAELTELPDGAVPYVLESGEGDRLLTGDQLHRIVAAQKNTDGQFIVVSSEGPKGDRIVDHYHEYHTETFYCLEGQmTmWTDGQEIQLNPGDFLHVPANTVHSYRLDSHYTKmVGVLVPGLFEPFFRTLGDPYEGHIFPCEPQALRFDRILQNIEALDLKVmKP 337
                                    12 |      22        32   |    42        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  |  
                                      14-MSE                36-MSE                                                                107-MSE     119-MSE                                                                                                                            250-MSE                             286-MSE                                          335-MSE
                                                                                                                                                                                                                                                                                   252-MSE
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H0V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H0V)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (QDOI_BACSU | P42106)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    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:0008127    quercetin 2,3-dioxygenase activity    Catalysis of the reaction: H(+) + O(2) + quercetin = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO.
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:336 - Pro A:337   [ RasMol ]  
    Lys B:336 - Pro B:337   [ RasMol ]  
    Val A:291 - Pro A:292   [ RasMol ]  
    Val B:291 - Pro B:292   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2h0v
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  QDOI_BACSU | P42106
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.13.11.24
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  QDOI_BACSU | P42106
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        QDOI_BACSU | P42106: 1y3t

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2H0V)