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(-) Description

Title :  CUMENE DIOXYGENASE (CUMA1A2) FROM PSEUDOMONAS FLUORESCENS IP01
 
Authors :  X. Dong, S. Fushinobu, E. Fukuda, T. Terada, S. Nakamura, K. Shimizu, H. T. Omori, H. Shoun, T. Wakagi
Date :  30 Sep 04  (Deposition) - 29 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Biphenyl Dioxygenase, Cumene Dioxygenase, Naphthalene Dioxygenase, Polychlorinated Biphenyl Degradation, Rieske Non-Heme Iron Dioxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Dong, S. Fushinobu, E. Fukuda, T. Terada, S. Nakamura, K. Shimizu, H. Nojiri, T. Omori, H. Shoun, T. Wakagi
Crystal Structure Of The Terminal Oxygenase Component Of Cumene Dioxygenase From Pseudomonas Fluorescens Ip01
J. Bacteriol. V. 187 2483 2005
PubMed-ID: 15774891  |  Reference-DOI: 10.1128/JB.187.7.2483-2490.2005

(-) Compounds

Molecule 1 - IRON-SULFUR PROTEIN LARGE SUBUNIT OF CUMENE DIOXYGENASE
    Chains: A
    EC Number: 1.14.12.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PUC118
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CUMA1
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 294
    Synonym: CUMENE DIOXYGENASE LARGE SUBUNIT
 
Molecule 2 - ETHYLBENZENE DIOXYGENASE SMALL SUBUNIT
    Chains: B
    EC Number: 1.14.12.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PUC118
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CUMA2
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 294
    Synonym: CUMENE DIOXYGENASE SMALL SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3OXY1Ligand/IonOXYGEN MOLECULE
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1FE23Ligand/IonFE (II) ION
2FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3OXY3Ligand/IonOXYGEN MOLECULE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:227 , HIS A:234 , HIS A:240 , ASP A:388 , OXY A:503BINDING SITE FOR RESIDUE FE2 A 502
2AC2SOFTWARECYS A:101 , HIS A:103 , ARG A:104 , CYS A:121 , TYR A:123 , HIS A:124 , TRP A:126BINDING SITE FOR RESIDUE FES A 501
3AC3SOFTWAREGLN A:227 , HIS A:234 , HIS A:240 , PHE A:378 , ASP A:388 , FE2 A:502BINDING SITE FOR RESIDUE OXY A 503

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:145 -A:152

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:327 -Pro A:328
2Asp B:103 -Pro B:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WQL)

(-) 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:436
 aligned with Q51743_PSEFL | Q51743 from UniProtKB/TrEMBL  Length:459

    Alignment length:441
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458 
         Q51743_PSEFL    19 NWSDEEIKALVDEEKGLLDPRIFSDQDLYEIELERVFARSWLLLGHEGHIPKAGDYLTTYMGEDPVIVVRQKDRSIKVFLNQCRHRGMRIERSDFGNAKSFTCTYHGWAYDTAGNLVNVPYEKEAFCDKKEGDCGFDKADWGPLQARVDTYKGLIFANWDTEAPDLKTYLSDATPYMDVMLDRTEAVTQVITGMQKTVIPCNWKFAAEQFCSDMYHAGTMAHLSGVLSSLPPEMDLSQVKLPSSGNQFRAKWGGHGTGWFNDDFALLQAIMGPKVVDYWTKGPAAERAKERLGKVLPADRMVAQHMTIFPTCSFLPGINTVRTWHPRGPNEIEVWSFIVVDADAPEDIKEEYRRKNIFTFNQGGTYEQDDGENWVEVQRGLRGYKARSRPLCAQMGAGVPNKNNPEFPGKTSYVYSEEAARGFYHHWSRMMSEPSWDTLKS 459
               SCOP domains d1wqla1 A:19-180 Large subunit of cumene dioxygenase cumA1                                                                                                        d1wqla2 A:181-459 Large subunit of cumene dioxygenase cumA1                                                                                                                                                                                                                             SCOP domains
               CATH domains 1wqlA01 A:19-57,A:189-459              1wqlA02 A:58-188 'Rieske'-like iron-sulphur domains                                                                                1wqlA01 A:19-57,A:189-459 Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------Rieske-1wqlA02 A:58-160                                                                                -----------------------Ring_hydroxyl_A-1wqlA01 A:184-451                                                                                                                                                                                                                                           -------- Pfam domains
         Sec.struct. author ..hhhhhhh.ee....ee.hhhhhhhhhhhhhhhhhhhhh.eeeee.hhh....eeeeeee..eeeeeee.....eeeee..............eee...ee......ee.....eee..hhhhhh..-----...hhhhh...eeeeeee..eeeee......hhhhhh..hhhhhhhhhh.....eee....eeeee..hhhhhhhhhhhhhhhhhh..hhhhhhhhh....hhhhh.....eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee...eee.....eeeeeee.....eeeeeeeeee...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..ee.................eeee...hhhhhhhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wql A  19 NWSDEEIKALVDEEKGLLDPRIFSDQDLYEIELERVFARSWLLLGHEGHIPKAGDYLTTYMGEDPVIVVRQKDRSIKVFLNQCRHRGMRIERSDFGNAKSFTCTYHGWAYDTAGNLVNVPYEKEAFCD-----CGFDKADWGPLQARVDTYKGLIFANWDTEAPDLKTYLSDATPYMDVMLDRTEAVTQVITGMQKTVIPCNWKFAAEQFCSDMYHAGTMAHLSGVLSSLPPEMDLSQVKLPSSGNQFRAKWGGHGTGWFNDDFALLQAIMGPKVVDYWTKGPAAERAKERLGKVLPADRMVAQHMTIFPTCSFLPGINTVRTWHPRGPNEIEVWSFIVVDADAPEDIKEEYRRKNIFTFNQGGTYEQDDGENWVEVQRGLRGYKARSRPLCAQMGAGVPNKNNPEFPGKTSYVYSEEAARGFYHHWSRMMSEPSWDTLKS 459
                                    28        38        48        58        68        78        88        98       108       118       128       138       | -   |   158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458 
                                                                                                                                                         146   152                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:182
 aligned with Q51744_PSEFL | Q51744 from UniProtKB/TrEMBL  Length:186

    Alignment length:182
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184  
         Q51744_PSEFL     5 DLTKPIEWPEMPVSLELQNAVEQFYYREAQLLDYQNYEAWLALLTQDIQYWMPIRTTHTSRNKAMEYVPPGGNAHFDETYESMRARIRARVSGLNWTEDPPSRSRHIVSNVIVRETESAGTLEVSSAFLCYRNRLERMTDIYVGERRDILLRVSDGLGFKIAKRTILLDQSTITANNLSQFF 186
               SCOP domains d1wqlb1 B:5-186 Small subunit of cumene dioxygenase CumA2                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------Ring_hydroxyl_B-1wqlB01 B:31-180                                                                                                                      ------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhh.hhhhhhh.......eeee.....hhhhhhhh.......eeeeehhhhhhhhhhhhh...hhhhh...eeeeeeeeeeeee.....eeeeeeeeeeeeee...eeeeeeeeeeeeeee......eeeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wql B   5 DLTKPIEWPEMPVSLELQNAVEQFYYREAQLLDYQNYEAWLALLTQDIQYWMPIRTTHTSRNKAMEYVPPGGNAHFDETYESMRARIRARVSGLNWTEDPPSRSRHIVSNVIVRETESAGTLEVSSAFLCYRNRLERMTDIYVGERRDILLRVSDGLGFKIAKRTILLDQSTITANNLSQFF 186
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184
   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  (3, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: Bet_V_1_like (93)
(-)
Clan: ISP-domain (54)
(-)
Clan: NTF2 (66)

(-) Gene Ontology  (12, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q51743_PSEFL | Q51743)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0016708    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and two atoms of oxygen are incorporated into one 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: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.

Chain B   (Q51744_PSEFL | Q51744)
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: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.
biological process
    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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  1wql
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  Q51743_PSEFL | Q51743
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  Q51744_PSEFL | Q51744
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  1.14.12.-
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