Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
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 HYDROXYQUINOL 1,2-DIOXYGENASE FROM NOCARDIOIDES SIMPLEX 3E
 
Authors :  M. Ferraroni, V. M. Travkin, J. Seifert, M. Schlomann, L. Golovleva, A. Scozzafava, F. Briganti
Date :  11 Jun 04  (Deposition) - 22 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Ferraroni, J. Seifert, V. M. Travkin, M. Thiel, S. Kaschabek, A. Scozzafava, L. Golovleva, M. Schlomann, F. Briganti
Crystal Structure Of The Hydroxyquinol 1, 2-Dioxygenase From Nocardioides Simplex 3E, A Key Enzyme Involved In Polychlorinated Aromatics Biodegradation.
J. Biol. Chem. V. 280 21144 2005
PubMed-ID: 15772073  |  Reference-DOI: 10.1074/JBC.M500666200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYDROXYQUINOL 1,2-DIOXYGENASE
    ChainsA, B
    EC Number1.13.11.37
    Organism ScientificPIMELOBACTER SIMPLEX
    Organism Taxid2045
    Strain3E

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
1BEZ2Ligand/IonBENZOIC ACID
2CL1Ligand/IonCHLORIDE ION
3CU1Ligand/IonCOPPER (II) ION
4FE2Ligand/IonFE (III) ION
5HGX2Ligand/Ion1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYLCHOLINE
6SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:164 , TYR A:197 , HIS A:221 , HIS A:223 , BEZ A:881BINDING SITE FOR RESIDUE FE A 861
02AC2SOFTWARETYR B:164 , TYR B:197 , HIS B:221 , HIS B:223 , BEZ B:882BINDING SITE FOR RESIDUE FE B 862
03AC3SOFTWAREHIS A:42 , CL A:891 , HIS B:42BINDING SITE FOR RESIDUE CU A 871
04AC4SOFTWAREHIS A:42 , CU A:871 , HOH A:1072 , HIS B:42BINDING SITE FOR RESIDUE CL A 891
05AC5SOFTWARETHR B:53 , ALA B:55 , HOH B:987 , HOH B:1050 , HOH B:1112 , HOH B:1264BINDING SITE FOR RESIDUE SO4 B 901
06AC6SOFTWARELYS A:255 , ASP A:256 , SER A:257 , HOH A:941 , HOH A:1160 , HOH A:1207BINDING SITE FOR RESIDUE SO4 A 902
07AC7SOFTWAREPHE A:46 , GLY A:60 , PHE A:63 , MET A:208 , HOH A:1112 , VAL B:35 , HGX B:852BINDING SITE FOR RESIDUE HGX A 851
08AC8SOFTWARELEU A:32 , HGX A:851 , GLU B:56 , TRP B:57 , THR B:59 , PHE B:63 , ALA B:211 , HOH B:1284 , HOH B:1297BINDING SITE FOR RESIDUE HGX B 852
09AC9SOFTWARELEU A:80 , ASP A:83 , GLY A:109 , PRO A:110 , PHE A:111 , TYR A:197 , ILE A:199 , ARG A:218 , HIS A:221 , HIS A:223 , FE A:861 , HOH A:908BINDING SITE FOR RESIDUE BEZ A 881
10BC1SOFTWAREASP B:83 , GLY B:109 , PRO B:110 , PHE B:111 , TYR B:197 , ILE B:199 , ARG B:218 , HIS B:221 , HIS B:223 , VAL B:251 , FE B:862 , HOH B:948BINDING SITE FOR RESIDUE BEZ B 882

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TMX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTRADIOL_DIOXYGENASPS00083 Intradiol ring-cleavage dioxygenases signature.CHQB_NOCSI136-164
 
  2A:136-164
B:136-164

(-) Exons   (0, 0)

(no "Exon" information available for 1TMX)

(-) 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:292
 aligned with CHQB_NOCSI | Q5PXQ6 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:292
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  
           CHQB_NOCSI     2 STPVSAEQQAREQDLVERVLRSFDATADPRLKQVMQALTRHLHAFLREVRLTEAEWETGIGFLTDAGHVTNERRQEFILLSDVLGASMQTIAMNNEAHGDATEATVFGPFFVEGSPRIESGGDIAGGAAGEPCWVEGTVTDTDGNPVPDARIEVWEADDDGFYDVQYDDDRTAARAHLLSGPDGGYAFWAITPTPYPIPHDGPVGRMLAATGRSPMRASHLHFMVTAPGRRTLVTHIFVEGDELLDRDSVFGVKDSLVKSFERQPAGAPTPGGREIDGPWSRVRFDIVLAPA 293
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..........................ee........eeeeeeeeee.........eeeee.......hhhhh.......eeeee.....eeeeeee....ee....hhhhhhhhhh....ee..eeeeeee......eeeeeee..hhhhhh......hhh.ee..eee.....hhhhh.....eeeee..eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tmx A   2 STPVSAEQQAREQDLVERVLRSFDATADPRLKQVMQALTRHLHAFLREVRLTEAEWETGIGFLTDAGHVTNERRQEFILLSDVLGASMQTIAMNNEAHGDATEATVFGPFFVEGSPRIESGGDIAGGAAGEPCWVEGTVTDTDGNPVPDARIEVWEADDDGFYDVQYDDDRTAARAHLLSGPDGGYAFWAITPTPYPIPHDGPVGRMLAATGRSPMRASHLHFMVTAPGRRTLVTHIFVEGDELLDRDSVFGVKDSLVKSFERQPAGAPTPGGREIDGPWSRVRFDIVLAPA 293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  

Chain B from PDB  Type:PROTEIN  Length:287
 aligned with CHQB_NOCSI | Q5PXQ6 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:290
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
           CHQB_NOCSI     4 PVSAEQQAREQDLVERVLRSFDATADPRLKQVMQALTRHLHAFLREVRLTEAEWETGIGFLTDAGHVTNERRQEFILLSDVLGASMQTIAMNNEAHGDATEATVFGPFFVEGSPRIESGGDIAGGAAGEPCWVEGTVTDTDGNPVPDARIEVWEADDDGFYDVQYDDDRTAARAHLLSGPDGGYAFWAITPTPYPIPHDGPVGRMLAATGRSPMRASHLHFMVTAPGRRTLVTHIFVEGDELLDRDSVFGVKDSLVKSFERQPAGAPTPGGREIDGPWSRVRFDIVLAPA 293
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------Dioxygenase_N-1tmxB03 B:29-106                                                Dioxygenase_C-1tmxB01 B:107-293                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) -------------------------Dioxygenase_N-1tmxB04 B:29-106                                                Dioxygenase_C-1tmxB02 B:107-293                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....................................eeeeeeeeee.........eeeee.......hhhhh.......eeeee.....eeeeeee....ee....hhhhhhhhhh....ee..eeeeeee......eeeeeee..hhhhhh......hhh.ee..ee..--......-......eeee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tmx B   4 PVSAEQQAREQDLVERVLRSFDATADPRLKQVMQALTRHLHAFLREVRLTEAEWETGIGFLTDAGHVTNERRQEFILLSDVLGASMQTIAMNNEAHGDATEATVFGPFFVEGSPRIESGGDIAGGAAGEPCWVEGTVTDTDGNPVPDARIEVWEADDDGFYDVQYDDDRTAARAHLLSGPDGGYAFWAITPTPYPIPHDGPVGRMLAATGRSPMRASHLHFMVTAPGRRTLVTHIFVEGDELLDRDSVFGVKDSLVKSFERQP--APTPGG-EIDGPWSRVRFDIVLAPA 293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  |  | 273| |    283       293
                                                                                                                                                                                                                                                                                                266  |  274 |                 
                                                                                                                                                                                                                                                                                                   269    276                 

   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 1TMX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1TMX)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CHQB_NOCSI | Q5PXQ6)
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: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:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0018581    hydroxyquinol 1,2-dioxygenase activity    Catalysis of the reaction: benzene-1,2,4-triol + O2 = 3-hydroxy-cis,cis-muconate.
    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: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: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:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0042952    beta-ketoadipate pathway    A pathway of aromatic compound degradation by ortho-cleavage; one branch converts protocatechuate, derived from phenolic compounds, to beta-ketoadipate, and the other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates.
    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.

 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
    BEZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HGX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tmx)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1tmx
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CHQB_NOCSI | Q5PXQ6
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.13.11.37
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CHQB_NOCSI | Q5PXQ6
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1TMX)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1TMX)