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 TOLUENE 2,3-DIOXYGENASE REDUCTASE
 
Authors :  R. Friemann, K. Lee, E. N. Brown, D. T. Gibson, H. Eklund, S. Ramaswamy
Date :  08 Sep 08  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Fad Binding Protein, Nadh Binding Protein, Aromatic Hydrocarbons Catabolism, Fad, Flavoprotein, Nad, 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--NAD(+) REDUCTASE
    Chains: A
    EC Number: 1.18.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDTG601A
    Expression System Strain: CGSC#7692
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PPUT_2878, TODA, TODC1C2BA
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 351746
    Strain: F1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL7Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:9 , GLY A:11 , VAL A:12 , GLY A:13 , GLY A:34 , ASP A:35 , GLU A:36 , ARG A:43 , PRO A:44 , SER A:47 , LYS A:48 , GLU A:79 , VAL A:80 , ALA A:106 , THR A:107 , GLY A:108 , ARG A:128 , ILE A:154 , LEU A:245 , GLY A:274 , ASP A:275 , GLU A:290 , THR A:291 , TYR A:292 , SER A:319 , TRP A:320 , GOL A:4124 , HOH A:4129 , HOH A:4131 , HOH A:4134 , HOH A:4139 , HOH A:4149 , HOH A:4152 , HOH A:4263BINDING SITE FOR RESIDUE FAD A 449
02AC2SOFTWARELEU A:153 , ILE A:154 , CYS A:236 , GLY A:238 , GOL A:4124 , GOL A:4125 , HOH A:4173 , HOH A:4276BINDING SITE FOR RESIDUE SO4 A4120
03AC3SOFTWAREALA A:369 , PRO A:370 , ARG A:371 , ASP A:372 , HOH A:4350 , HOH A:4470BINDING SITE FOR RESIDUE SO4 A4121
04AC4SOFTWAREPRO A:117 , GLY A:118 , GLN A:120 , LEU A:121BINDING SITE FOR RESIDUE GOL A4122
05AC5SOFTWARELEU A:153 , ARG A:287 , LEU A:289 , PRO A:317 , HOH A:4140 , HOH A:4218 , HOH A:4239 , HOH A:4392BINDING SITE FOR RESIDUE GOL A4123
06AC6SOFTWAREARG A:128 , ASP A:275 , GLU A:290 , FAD A:449 , SO4 A:4120 , HOH A:4157 , HOH A:4174 , HOH A:4276BINDING SITE FOR RESIDUE GOL A4124
07AC7SOFTWAREALA A:111 , LEU A:127 , ILE A:235 , CYS A:236 , VAL A:237 , GLY A:238 , SO4 A:4120 , HOH A:4174BINDING SITE FOR RESIDUE GOL A4125
08AC8SOFTWAREASP A:42 , PRO A:44 , SER A:45 , LYS A:48 , TRP A:320 , GLU A:322 , ARG A:327 , HOH A:4165 , HOH A:4403 , HOH A:4588BINDING SITE FOR RESIDUE GOL A4126
09AC9SOFTWAREPRO A:37 , HIS A:38 , HOH A:4208 , HOH A:4441BINDING SITE FOR RESIDUE GOL A4127
10BC1SOFTWARETYR A:292 , GLN A:296 , HOH A:4290BINDING SITE FOR RESIDUE GOL A4128

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EF6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EF6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EF6)

(-) Exons   (0, 0)

(no "Exon" information available for 3EF6)

(-) 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:400
 aligned with TODA_PSEP1 | A5W4E9 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:400
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402
           TODA_PSEP1     3 THVAIIGNGVGGFTTAQALRAEGFEGRISLIGDEPHLPYDRPSLSKAVLDGSLERPPILAEADWYGEARIDMLTGPEVTALDVQTRTISLDDGTTLSADAIVIATGSRARTMALPGSQLPGVVTLRTYGDVQVLRDSWTSATRLLIVGGGLIGCEVATTARKLGLSVTILEAGDELLVRVLGRRIGAWLRGLLTELGVQVELGTGVVGFSGEGQLEQVMASDGRSFVADSALICVGAEPADQLARQAGLACDRGVIVDHCGATLAKGVFAVGDVASWPLRAGGRRSLETYMNAQRQAAAVAAAILGKNVSAPQLPVSWTEIAGHRMQMAGDIEGPGDFVSRGMPGSGAALLFRLQERRIQAVVAVDAPRDFALATRLVEARAAIEPARLADLSNSMRDFV 402
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh....eeeeee........hhhhhh................hhhhhh..eeee...eeeee....eeee....eee..eeee...eee............ee...hhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhh.eee....eeeee......eeee....eee..eeee...eee.hhhhhhh.......ee...........eee....eeee.....ee...hhhhhhhhhhhhhhhhh..........eeeeee..eeeeee.......eeeee.......eeeeeee..eeeeeeee.hhhhhhhhhhhhhhh...hhhhhhh...hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ef6 A   3 THVAIIGNGVGGFTTAQALRAEGFEGRISLIGDEPHLPYDRPSLSKAVLDGSLERPPILAEADWYGEARIDMLTGPEVTALDVQTRTISLDDGTTLSADAIVIATGSRARTMALPGSQLPGVVTLRTYGDVQVLRDSWTSATRLLIVGGGLIGCEVATTARKLGLSVTILEAGDELLVRVLGRRIGAWLRGLLTELGVQVELGTGVVGFSGEGQLEQVMASDGRSFVADSALICVGAEPADQLARQAGLACDRGVIVDHCGATLAKGVFAVGDVASWPLRAGGRRSLETYMNAQRQAAAVAAAILGKNVSAPQLPVSWTEIAGHRMQMAGDIEGPGDFVSRGMPGSGAALLFRLQERRIQAVVAVDAPRDFALATRLVEARAAIEPARLADLSNSMRDFV 402
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402
   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 3EF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EF6)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TODA_PSEP1 | A5W4E9)
molecular function
    GO:0008860    ferredoxin-NAD+ reductase activity    Catalysis of the reaction: reduced ferredoxin + NAD+ = oxidized ferredoxin + NADH + H+.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

 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
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ 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 3ef6)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ef6
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TODA_PSEP1 | A5W4E9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.18.1.3
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TODA_PSEP1 | A5W4E9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TODA_PSEP1 | A5W4E9: 4emi 4emj

(-) Related Entries Specified in the PDB File

3dqy STRUCTURE OF THE TOLUENE 2,3-DIOXYGENASE FERREDOXIN COMPONENT
3en1 STRUCTURE OF THE TOLUENE 2,3-DIOXYGENASE COMPONENT
3eqq STRUCTURE OF THE APO-TOLUENE 2,3-DIOXYGENASE COMPONENT