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(-) Description

Title :  CRYSTAL STRUCTURE OF YXAG, A DIOXYGENASE FROM BACILLUS SUBTILIS
 
Authors :  B. Gopal, L. L. Madan, S. F. Betz, A. A. Kossiakoff
Date :  26 Nov 04  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bi Cupin, Dioxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Gopal, L. L. Madan, S. F. Betz, A. A. Kossiakoff
The Crystal Structure Of A Quercetin 2, 3-Dioxygenase From Bacillus Subtilis Suggests Modulation Of Enzyme Activity By A Change In The Metal Ion At The Active Site(S)
Biochemistry V. 44 193 2005
PubMed-ID: 15628860  |  Reference-DOI: 10.1021/BI0484421
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YXAG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B-YXAG
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YXAG
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1FE4Ligand/IonFE (III) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:62 , HIS A:64 , GLU A:69 , HIS A:103 , HOH A:469BINDING SITE FOR RESIDUE FE A 401
2AC2SOFTWAREHIS A:234 , HIS A:236 , GLU A:241 , HIS A:275 , HOH A:445BINDING SITE FOR RESIDUE FE A 402
3AC3SOFTWAREHIS B:62 , HIS B:64 , GLU B:69 , HIS B:103 , HOH B:452 , HOH B:525BINDING SITE FOR RESIDUE FE B 401
4AC4SOFTWAREHIS B:234 , HIS B:236 , GLU B:241 , HIS B:275 , HOH B:426 , HOH B:458BINDING SITE FOR RESIDUE FE B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y3T)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Arg A:151 -Phe A:152
2Val A:291 -Pro A:292
3Val B:291 -Pro B:292

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y3T)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y3T)

(-) 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:330
 aligned with QDOI_BACSU | P42106 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:330
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334
           QDOI_BACSU     5 CTHSLPKEKMPYLLRSGEGERYLFGRQVATVMANGRSTGDLFEIVLLSGGKGDAFPLHVHKDTHEGILVLDGKLELTLDGERYLLISGDYANIPAGTPHSYRMQSHRTRLVSYTMKGNVAHLYSVIGNPYDHAEHPPYASEEVSNERFAEAAAVADIVFLDEAKPACSAKLAELTELPDGAVPYVLESGEGDRLLTGDQLHRIVAAQKNTDGQFIVVSSEGPKGDRIVDHYHEYHTETFYCLEGQMTMWTDGQEIQLNPGDFLHVPANTVHSYRLDSHYTKMVGVLVPGLFEPFFRTLGDPYEGHIFPCEPQALRFDRILQNIEALDLKV 334
               SCOP domains d1y3ta1 A:5-334 Hypothetical protein YxaG                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eee.....eeeee..eeeeeeehhhhhh..eeeeeeee....eeeeee.....eeeeeee..eeeee..eeeee....eeee.....eeeee....eeeeeeee....hhhhhhhhee..................hhhhh...ee............ee............eee.....eeeee..eeeeeeehhhhh....eeeeeee........ee....eeeeeeee..eeeee..eeeee....eeee.....eeeee....eeeeeeee....hhhhhhhhee.............hhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y3t A   5 CTHSLPKEKMPYLLRSGEGERYLFGRQVATVMANGRSTGDLFEIVLLSGGKGDAFPLHVHKDTHEGILVLDGKLELTLDGERYLLISGDYANIPAGTPHSYRMQSHRTRLVSYTMKGNVAHLYSVIGNPYDHAEHPPYASEEVSNERFAEAAAVATIVFLDEAKPACSAKLAELTELPDGAVPYVLESGEGDRLLTGDQLHRIVAAQKNTDGQFIVVSSEGPKGDRIVDHYHEYHTETFYCLEGQMTMWTDGQEIQLNPGDFLHVPANTVHSYRLDSHYTKMVGVLVPGLFEPFFRTLGDPYEGHIFPCKPQALRFDRILQNIEALDLKV 334
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with QDOI_BACSU | P42106 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:330
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334
           QDOI_BACSU     5 CTHSLPKEKMPYLLRSGEGERYLFGRQVATVMANGRSTGDLFEIVLLSGGKGDAFPLHVHKDTHEGILVLDGKLELTLDGERYLLISGDYANIPAGTPHSYRMQSHRTRLVSYTMKGNVAHLYSVIGNPYDHAEHPPYASEEVSNERFAEAAAVADIVFLDEAKPACSAKLAELTELPDGAVPYVLESGEGDRLLTGDQLHRIVAAQKNTDGQFIVVSSEGPKGDRIVDHYHEYHTETFYCLEGQMTMWTDGQEIQLNPGDFLHVPANTVHSYRLDSHYTKMVGVLVPGLFEPFFRTLGDPYEGHIFPCEPQALRFDRILQNIEALDLKV 334
               SCOP domains d1y3tb_ B: Hypothetical protein YxaG                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_2-1y3tB01 B:223-291                                            ------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_2-1y3tB02 B:223-291                                            ------------------------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_2-1y3tB03 B:223-291                                            ------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_2-1y3tB04 B:223-291                                            ------------------------------------------- Pfam domains (4)
         Sec.struct. author ...........eee.....eeeee..eeeeeeehhhhhh..eeeeeeee....eeeeee.....eeeeeee..eeeee..eeeee....eeee.....eeeee....eeeeeeee.....hhhhhhhee..................hhhhhh..ee............ee............eee.....eeeee..eeeeeeehhhhh....eeeeeee........ee.....eeeeeee..eeeee..eeeee....eeee.....eeeee....eeeeeee....hhhhhhhhhee.............hhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y3t B   5 CTHSLPKEKMPYLLRSGEGERYLFGRQVATVMANGRSTGDLFEIVLLSGGKGDAFPLHVHKDTHEGILVLDGKLELTLDGERYLLISGDYANIPAGTPHSYRMQSHRTRLVSYTMKGNVAHLYSVIGNPYDHAEHPPYASEEVSNERFAEAAAVATIVFLDEAKPACSAKLAELTELPDGAVPYVLESGEGDRLLTGDQLHRIVAAQKNTDGQFIVVSSEGPKGDRIVDHYHEYHTETFYCLEGQMTMWTDGQEIQLNPGDFLHVPANTVHSYRLDSHYTKMVGVLVPGLFEPFFRTLGDPYEGHIFPCKPQALRFDRILQNIEALDLKV 334
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334
   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 1Y3T)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)
(-)
Family: Cupin_2 (16)
(-)
Bacillus subtilis (1)
1aCupin_2-1y3tB01B:223-291
1bCupin_2-1y3tB02B:223-291
1cCupin_2-1y3tB03B:223-291
1dCupin_2-1y3tB04B:223-291

(-) 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.

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        QDOI_BACSU | P42106: 2h0v

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