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(-) Description

Title :  CRYATAL STRUCTURE OF HYDROXYQUINOL 1,2-DIOXYGENASE FROM PSEUDOMONAS PUTIDA DLL-E4
 
Authors :  W. Liu, W. Shen, P. Fang, J. Li, Z. Cui
Date :  31 May 10  (Deposition) - 04 Aug 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Phospholipid Binds, N-Terminal Helix Tunnel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Liu, W. Shen, P. Fang, J. Li, Z. Cui
Cryatal Structure Of Hydroxyquinol 1, 2-Dioxygenase From Pseudomonas Putida Dll-E4
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PNPC
    Chains: A
    EC Number: 1.13.11.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B
    Expression System Strain: BL21(DE3))
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PNPC
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Strain: DLL-E4
    Synonym: HYDROXYQUINOL 1,2-DIOXYGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2FLC1Ligand/IonCITRATE ANION
3HGX1Ligand/Ion1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYLCHOLINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2FLC2Ligand/IonCITRATE ANION
3HGX2Ligand/Ion1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYLCHOLINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:24 , ASN A:25 , PHE A:28 , GLU A:52 , TRP A:53 , ILE A:57 , PHE A:59 , PHE A:75 , LEU A:78 , GLN A:140 , ARG A:142 , ALA A:208BINDING SITE FOR RESIDUE HGX A 300
2AC2SOFTWARELEU A:77 , ASP A:80 , PRO A:107 , PHE A:108 , TYR A:160 , TYR A:194 , ILE A:196 , PRO A:197 , ARG A:215 , HIS A:218 , HIS A:220 , VAL A:248 , FE A:292 , HOH A:313BINDING SITE FOR RESIDUE FLC A 293
3AC3SOFTWARETYR A:160 , TYR A:194 , HIS A:218 , HIS A:220 , FLC A:293 , HOH A:313BINDING SITE FOR RESIDUE FE A 292

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N9T)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:5 -Lys A:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N9T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N9T)

(-) Exons   (0, 0)

(no "Exon" information available for 3N9T)

(-) 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:286
 aligned with C6FI44_PSEPU | C6FI44 from UniProtKB/TrEMBL  Length:290

    Alignment length:286
                                    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      
         C6FI44_PSEPU     5 YKAVEALISDQAVDSFETSPNPRFKQIMQSLVRHLHDFVSEVELTEQEWFEGIRFLTATGQKCDGKVRQEFILLSDTLGVSMLVDAINHRQSTNATETTVFGPFFIEGMPDRGYGENMALTDGVPALVYGRVLDVQGRPVVGAVLDVWQTADNGMYSGQDPDQPFGNLRGRYRSDNDGCFAIQTTVPVCYPIPTDGPVGEMLDAANRHAWRPAHLHFMIQAPGYRKLVTHLFNSDDPYLDSDAVFGVKGSLQVKYEDRPAHDEDAGGLDMPYPYKSAYYEFVMEAE 290
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------Dioxygenase_N-3n9tA02 A:25-100                                              ---Dioxygenase_C-3n9tA01 A:104-289                                                                                                                                                           - Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....................................eeeeeeeeee.........eeeee....................eeeee.....eeeeeee....ee....hhhhhhhhhhh...ee..eeeeeee......eeeeeee..............hhh.ee..eee...............eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9t A   5 YKAVEALISDQAVDSFETSPNPRFKQIMQSLVRHLHDFVSEVELTEQEWFEGIRFLTATGQKCDGKVRQEFILLSDTLGVSMLVDAINHRQSTNATETTVFGPFFIEGMPDRGYGENMALTDGVPALVYGRVLDVQGRPVVGAVLDVWQTADNGMYSGQDPDQPFGNLRGRYRSDNDGCFAIQTTVPVCYPIPTDGPVGEMLDAANRHAWRPAHLHFMIQAPGYRKLVTHLFNSDDPYLDSDAVFGVKGSLQVKYEDRPAHDEDAGGLDMPYPYKSAYYEFVMEAE 290
                                    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
   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 3N9T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N9T)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Transthyretin (88)
(-)
Clan: no clan defined [family: Dioxygenase_N] (6)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (C6FI44_PSEPU | C6FI44)
molecular function
    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:0018576    catechol 1,2-dioxygenase activity    Catalysis of the reaction: catechol + O2 = cis,cis-muconate.
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016702    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
biological process
    GO:0009712    catechol-containing compound metabolic process    The chemical reactions and pathways involving a compound containing a pyrocatechol (1,2-benzenediol) nucleus or substituent.
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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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