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(-) Description

Title :  CRYSTAL STRUCTURE OF TOLUENE 2,3-DIOXYGENASE FERREDOXIN
 
Authors :  R. Friemann, K. Lee, E. N. Brown, D. T. Gibson, H. Eklund, S. Ramaswamy
Date :  10 Jul 08  (Deposition) - 10 Mar 09  (Release) - 10 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Rieske, Iron-Sulfur Cluster, 2Fe-2S, Aromatic Hydrocarbons Catabolism, Electron Transport, Iron, Iron-Sulfur, Metal- Binding, Transport, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Friemann, K. Lee, E. N. Brown, D. T. Gibson, H. Eklund, S. Ramaswamy
Structures Of The Multicomponent Rieske Non-Heme Iron Toluene 2, 3-Dioxygenase Enzyme System
Acta Crystallogr. , Sect. D V. 65 24 2009
PubMed-ID: 19153463  |  Reference-DOI: 10.1107/S0907444908036524
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TOLUENE 1,2-DIOXYGENASE SYSTEM FERREDOXIN SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDTG614
    Expression System Strain: JM109
    Expression System Vector Type: PLASMID
    Gene: TODB
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Strain: F1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:42 , HIS A:44 , GLY A:45 , CYS A:61 , HIS A:64 , GLY A:66BINDING SITE FOR RESIDUE FES A 107

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIESKEPS51296 Rieske [2Fe-2S] iron-sulfur domain profile.TODB_PSEP14-99  1A:3-98
TODB_PSEPU4-99  1A:3-98

(-) Exons   (0, 0)

(no "Exon" information available for 3DQY)

(-) 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:106
 aligned with TODB_PSEP1 | A5W4F0 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           TODB_PSEP1     2 TWTYILRQGDLPPGEMQRYEGGPEPVMVCNVDGEFFAVQDTCTHGDWALSDGYLDGDIVECTLHFGKFCVRTGKVKALPACKPIKVFPIKVEGDEVHVDLDNGELK 107
               SCOP domains d3dqya_ A: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh....eeee......eeeeee..eeeeee........hhhhheee..eee......eee.....eee........ee.eeee..eeee.hhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RIESKE  PDB: A:3-98 UniProt: 4-99                                                               -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3dqy A   1 TWTYILRQGDLPPGEMQRYEGGPEPVMVCNVDGEFFAVQDTCTHGDWALSDGYLDGDIVECTLHFGKFcVRTGKVKALPACKPIKVFPIKVEGDEVHVDLDNGELK 106
                                    10        20        30        40        50        60        70        80        90       100      
                                                                                               69-CSO                                 


Chain A from PDB  Type:PROTEIN  Length:106
 aligned with TODB_PSEPU | P0C620 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           TODB_PSEPU     2 TWTYILRQGDLPPGEMQRYEGGPEPVMVCNVDGEFFAVQDTCTHGDWALSDGYLDGDIVECTLHFGKFCVRTGKVKALPACKPIKVFPIKVEGDEVHVDLDNGELK 107
               SCOP domains d3dqya_ A: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh....eeee......eeeeee..eeeeee........hhhhheee..eee......eee.....eee........ee.eeee..eeee.hhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --RIESKE  PDB: A:3-98 UniProt: 4-99                                                               -------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3dqy A   1 TWTYILRQGDLPPGEMQRYEGGPEPVMVCNVDGEFFAVQDTCTHGDWALSDGYLDGDIVECTLHFGKFcVRTGKVKALPACKPIKVFPIKVEGDEVHVDLDNGELK 106
                                    10        20        30        40        50        60        70        80        90       100      
                                                                                               69-CSO
   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DQY)

(-) Gene Ontology  (7, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TODB_PSEPU | P0C620)
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: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.
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: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.
    GO:0042203    toluene catabolic process    The chemical reactions and pathways resulting in the breakdown of toluene, a volatile monoaromatic hydrocarbon found in crude petroleum and petroleum products.

Chain A   (TODB_PSEP1 | A5W4F0)
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: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.
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: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.
    GO:0042203    toluene catabolic process    The chemical reactions and pathways resulting in the breakdown of toluene, a volatile monoaromatic hydrocarbon found in crude petroleum and petroleum products.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TODB_PSEP1 | A5W4F0: 4emj
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(-) Related Entries Specified in the PDB File

3ef6 STRUCTURE OF TOLUENE 2,3-DIOXYGENASE REDUCTASE COMPONENT
3en1 STRUCTURE OF THE TOLUENE 2,3-DIOXYGENASE COMPONENT
3eqq STRUCTURE OF THE APO-TOLUENE 2,3-DIOXYGENASE COMPONENT