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(-) Description

Title :  CRYSTAL STRUCTURE OF 4-CHLOROCATECHOL 1,2-DIOXYGENASE FROM RHODOCOCCUS OPACUS 1CP
 
Authors :  M. Ferraroni, I. P. Solyanikova, M. P. Kolomytseva, A. Scozzafava, L. A. Golovleva, F. Briganti
Date :  04 Feb 04  (Deposition) - 01 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.47
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ferraroni, I. P. Solyanikova, M. P. Kolomytseva, A. Scozzafava, L. Golovleva, F. Briganti
Crystal Structure Of 4-Chlorocatechol 1, 2-Dioxygenase From The Chlorophenol-Utilizing Gram-Positive Rhodococcus Opacus 1Cp.
J. Biol. Chem. V. 279 27646 2004
PubMed-ID: 15060064  |  Reference-DOI: 10.1074/JBC.M401692200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHLOROCATECHOL 1,2-DIOXYGENASE
    Chains: A, B
    EC Number: 1.13.11.1
    Organism Scientific: RHODOCOCCUS OPACUS
    Organism Taxid: 37919
    Strain: 1CP
    Synonym: PYROCATECHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1BEZ2Ligand/IonBENZOIC ACID
2FE2Ligand/IonFE (III) ION
3HGP2Ligand/Ion(1-HEXADECANOYL-2-TETRADECANOYL-GLYCEROL-3-YL)PHOSPHONYL CHOLINE
4TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:134 , TYR A:169 , HIS A:194 , HIS A:196 , BEZ A:306BINDING SITE FOR RESIDUE FE A 300
2AC2SOFTWARETYR B:134 , TYR B:169 , HIS B:194 , HIS B:196 , BEZ B:307BINDING SITE FOR RESIDUE FE B 301
3AC3SOFTWARETHR A:33 , TYR A:37 , TRP A:50 , TYR A:184 , HGP A:304 , ALA B:2 , VAL B:6 , LEU B:9 , PHE B:13BINDING SITE FOR RESIDUE HGP B 303
4AC4SOFTWAREASN A:3 , VAL A:6 , PHE A:13 , PHE B:20 , THR B:33 , TYR B:37 , TRP B:50 , TYR B:184 , HGP B:303BINDING SITE FOR RESIDUE HGP A 304
5AC5SOFTWAREPRO A:48 , ASP A:52 , GLU A:56 , GLN A:75 , GLY A:76 , PRO A:77 , HOH A:451 , THR B:28 , GLU B:32 , MET B:35BINDING SITE FOR RESIDUE TAM A 305
6AC6SOFTWARELEU A:49 , ASP A:52 , ALA A:53 , ILE A:74 , GLY A:76 , PRO A:77 , PHE A:78 , TYR A:134 , TYR A:169 , ARG A:191 , HIS A:194 , HIS A:196 , CYS A:224 , FE A:300BINDING SITE FOR RESIDUE BEZ A 306
7AC7SOFTWARELEU B:49 , ILE B:74 , GLY B:76 , PRO B:77 , PHE B:78 , TYR B:134 , TYR B:169 , ARG B:191 , HIS B:194 , HIS B:196 , CYS B:224 , FE B:301BINDING SITE FOR RESIDUE BEZ B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S9A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S9A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S9A)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTRADIOL_DIOXYGENASPS00083 Intradiol ring-cleavage dioxygenases signature.CLCA_RHOOP106-134
 		  2A:106-134
B:106-134

(-) Exons   (0, 0)

(no "Exon" information available for 1S9A)

(-) 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:256
 aligned with CLCA_RHOOP | O67987 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:256
                                    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      
           CLCA_RHOOP     2 ANTRVIELFDEFTDLIRDFIVRHEITTPEYETIMQYMISVGEAGEWPLWLDAFFETTVDSVSYGKGNWTSSAIQGPFFKEGAPLLTGKPATLPMRADEPGDRMRFTGSVRDTSGTPITGAVIDVWHSTNDGNYSFFSPALPDQYLLRGRVVPAEDGSIEFHSIRPVPYEIPKAGPTGQLMNSYLGRHSWRPAHIHIRITADGYRPLITQLYFEGDPYLDSDSCSAVKSELVLPVNKIDIDGETWQLVDFNFILQHN 257
               SCOP domains d1s9aa_ A: Chlorocatechol 1,2-dioxygenase                                                                                                                                                                                                                        SCOP domains
               CATH domains 1s9aA00 A:2-257 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....................ee................eeeeeeeeee.........eeeee.....................eeee......eeeeeee....ee....hhhhhhhhh......ee..eeeeeeee..eeeeeeeeee..............hhh.ee..ee........eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9a A   2 ANTRVIELFDEFTDLIRDFIVRHEITTPEYETIMQYMISVGEAGEWPLWLDAFFETTVDSVSYGKGNWTSSAIQGPFFKEGAPLLTGKPATLPMRADEPGDRMRFTGSVRDTSGTPITGAVIDVWHSTNDGNYSFFSPALPDQYLLRGRVVPAEDGSIEFHSIRPVPYEIPKAGPTGQLMNSYLGRHSWRPAHIHIRITADGYRPLITQLYFEGDPYLDSDSCSAVKSELVLPVNKIDIDGETWQLVDFNFILQHN 257
                                    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      


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with CLCA_RHOOP | O67987 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:256
                                    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      
           CLCA_RHOOP     2 ANTRVIELFDEFTDLIRDFIVRHEITTPEYETIMQYMISVGEAGEWPLWLDAFFETTVDSVSYGKGNWTSSAIQGPFFKEGAPLLTGKPATLPMRADEPGDRMRFTGSVRDTSGTPITGAVIDVWHSTNDGNYSFFSPALPDQYLLRGRVVPAEDGSIEFHSIRPVPYEIPKAGPTGQLMNSYLGRHSWRPAHIHIRITADGYRPLITQLYFEGDPYLDSDSCSAVKSELVLPVNKIDIDGETWQLVDFNFILQHN 257
               SCOP domains d1s9ab_ B: Chlorocatechol 1,2-dioxygenase                                                                                                                                                                                                                        SCOP domains
               CATH domains 1s9aB00 B:2-257 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                                       CATH domains
           Pfam domains (1) -Dioxygenase_N-1s9aB03 B:3-68                                      -----Dioxygenase_C-1s9aB01 B:74-257                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) -Dioxygenase_N-1s9aB04 B:3-68                                      -----Dioxygenase_C-1s9aB02 B:74-257                                                                                                                                                           Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......................................eeeeeeeeee.........eeeee.....................eeee......eeeeeee....ee....hhhhhhhhh......ee..eeeeeee......eeeeeee..............hhh.ee..ee........eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9a B   2 ANTRVIELFDEFTDLIRDFIVRHEITTPEYETIMQYMISVGEAGEWPLWLDAFFETTVDSVSYGKGNWTSSAIQGPFFKEGAPLLTGKPATLPMRADEPGDRMRFTGSVRDTSGTPITGAVIDVWHSTNDGNYSFFSPALPDQYLLRGRVVPAEDGSIEFHSIRPVPYEIPKAGPTGQLMNSYLGRHSWRPAHIHIRITADGYRPLITQLYFEGDPYLDSDSCSAVKSELVLPVNKIDIDGETWQLVDFNFILQHN 257
                                    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
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CLCA_RHOOP | O67987)
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:0018575    chlorocatechol 1,2-dioxygenase activity    Catalysis of the reaction: 3,6-dichlorocatechol + O2 = 2 H+ + 2,5-dichloro-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: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: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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  1s9a
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 Related Entries

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

UniProtKB/Swiss-Prot
        CLCA_RHOOP | O67987: 3o32 3o5u 3o6j 3o6r

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