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(-) Description

Title :  CRYSTAL STRUCTURE OF 2,2',3-TRIHYDROXYBIPHENYL 1,2-DIOXYGENASE FROM DIBENZOFURAN-DEGRADING SPHINGOMONAS WITTICHII STRAIN RW1
 
Authors :  M. Koksal, P. Kumar, J. T. Bolin
Date :  30 Dec 11  (Deposition) - 03 Apr 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Translational Non-Crystallographic Symmetry, Hypersymmetry, Unusual Crystal Packing, Extradiol Dioxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Koksal, P. Kumar, P. D. Fortin, L. D. Eltis, J. T. Bolin
Crystal Structure Of A Dibenzofuran-Degrading Dioxygenase: An Unusual Spatially Heterogeneous Crystal With A Hypersymmetric Intensity Distribution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYOXALASE/BLEOMYCIN RESISTANCE PROTEIN/DIOXYGENASE
    Chains: A, B, C, D
    EC Number: 1.13.11.-
    Engineered: YES
    Expression System: PSEUDOMONAS PUTIDA
    Expression System Plasmid: PAHD1
    Expression System Strain: KT2442
    Expression System Taxid: 303
    Expression System Vector Type: PLASMID
    Gene: DBFB, SWIT_4902
    Organism Scientific: SPHINGOMONAS WITTICHII
    Organism Taxid: 392499
    Strain: RW1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1FE24Ligand/IonFE (II) ION
2P6G2Ligand/IonHEXAETHYLENE GLYCOL
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2P6G1Ligand/IonHEXAETHYLENE GLYCOL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2P6G1Ligand/IonHEXAETHYLENE GLYCOL
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2P6G-1Ligand/IonHEXAETHYLENE GLYCOL
3SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2P6G-1Ligand/IonHEXAETHYLENE GLYCOL
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:147 , HIS A:209 , TYR A:250 , GLU A:260 , HOH A:501 , HOH A:502BINDING SITE FOR RESIDUE FE2 A 301
2AC2SOFTWAREGLN A:20 , VAL A:24 , GLU A:79 , GLY A:231 , TYR A:232 , ASP A:233 , MET A:252 , PRO A:254 , HOH A:568 , GLU C:137BINDING SITE FOR RESIDUE P6G A 302
3AC3SOFTWAREGLN A:5 , ARG A:51 , PHE A:123 , GLY A:136 , GLU A:137 , HOH A:506 , GLN D:219 , ARG D:222BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREHIS B:147 , HIS B:209 , TYR B:250 , GLU B:260 , HOH B:501 , HOH B:502BINDING SITE FOR RESIDUE FE2 B 301
5AC5SOFTWAREGLN B:20 , VAL B:24 , GLU B:79 , GLY B:231 , TYR B:232 , ASP B:233 , MET B:251 , MET B:252 , PRO B:254 , HOH B:568 , ASN C:60 , GLY C:201 , LEU C:202 , LYS C:203 , MET C:206 , VAL C:207 , HIS C:208 , ALA C:255 , PHE C:257BINDING SITE FOR RESIDUE P6G B 302
6AC6SOFTWAREGLN B:5 , ARG B:51 , PHE B:123 , GLY B:136 , GLU B:137 , HOH B:506 , ASP D:16 , GLN D:20 , ALA D:78 , GLU D:82 , VAL D:88BINDING SITE FOR RESIDUE SO4 B 303
7AC7SOFTWAREHIS C:147 , HIS C:209 , TYR C:250 , GLU C:260BINDING SITE FOR RESIDUE FE2 C 300
8AC8SOFTWAREHIS D:147 , HIS D:209 , TYR D:250 , GLU D:260BINDING SITE FOR RESIDUE FE2 D 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VB0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VB0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VB0)

(-) Exons   (0, 0)

(no "Exon" information available for 3VB0)

(-) 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:289
 aligned with A5VGW5_SPHWW | A5VGW5 from UniProtKB/TrEMBL  Length:294

    Alignment length:289
                                    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         
         A5VGW5_SPHWW     2 SVKQLGYLIFECRADVLEQMVVVYQDIIGAVVERDEGGRALVRLDGRPFRIRLDPGPANRLAAIGWNVDPSDLAAIAEQVEKACYSVVTADAELAADRAAAQVRQFADNDGFTHELYVESSFPTDPVLESLFVCGEEANGIFGLGHLVVIVADRAKTQSFFTDVLGFGLSDRVTWPEADIFFLHCNQRHHTVALSAPALGLKPGMVHHLMLEAKSKEQVDRAFAAVKRLGYDVLMTIGQHSNDKVYSFYMMAPAGFAVELGFGGQVIGDLESWHVGFYDAPSIWGHELQ 290
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhhhhhhhhhhhhhh...eeee.....eeee.......eeeee....eeeeeeee.hhhhhhhhhhhhhhh....ee.hhhhhhhh.eeeeeeee.....eeeeeee.....hhhhhh.....ee..ee....eeeee..hhhhhhhhhhhh...eeeeeeee..eeeeeee.......eeee..........eeeeeee..hhhhhhhhhhhhhhh.....eeeeee.....eeeeee.....eeeeee......hhhhh..eee...eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vb0 A   2 SVKQLGYLIFECRADVLEQMVVVYQDIIGAVVERDEGGRALVRLDGRPFRIRLDPGPANRLAAIGWNVDPSDLAAIAEQVEKACYSVVTADAELAADRAAAQVRQFADNDGFTHELYVESSFPTDPVLESLFVCGEEANGIFGLGHLVVIVADRAKTQSFFTDVLGFGLSDRVTWPEADIFFLHCNQRHHTVALSAPALGLKPGMVHHLMLEAKSKEQVDRAFAAVKRLGYDVLMTIGQHSNDKVYSFYMMAPAGFAVELGFGGQVIGDLESWHVGFYDAPSIWGHELQ 290
                                    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         


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with A5VGW5_SPHWW | A5VGW5 from UniProtKB/TrEMBL  Length:294

    Alignment length:289
                                    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         
         A5VGW5_SPHWW     2 SVKQLGYLIFECRADVLEQMVVVYQDIIGAVVERDEGGRALVRLDGRPFRIRLDPGPANRLAAIGWNVDPSDLAAIAEQVEKACYSVVTADAELAADRAAAQVRQFADNDGFTHELYVESSFPTDPVLESLFVCGEEANGIFGLGHLVVIVADRAKTQSFFTDVLGFGLSDRVTWPEADIFFLHCNQRHHTVALSAPALGLKPGMVHHLMLEAKSKEQVDRAFAAVKRLGYDVLMTIGQHSNDKVYSFYMMAPAGFAVELGFGGQVIGDLESWHVGFYDAPSIWGHELQ 290
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhhhhhhhhhhhhhh...eeee.....eeee.......eeeee....eeeeeeee.hhhhhhhhhhhhhhh....ee.hhhhhhhh.eeeeeeee.....eeeeeee.....hhhhhh.....ee..ee....eeeee..hhhhhhhhhhhh...eeeeeeee..eeeeeee.......eeee..........eeeeeee..hhhhhhhhhhhhhhh.....eeeeee.....eeeeee.....eeeeee......hhhhh..eee...eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vb0 B   2 SVKQLGYLIFECRADVLEQMVVVYQDIIGAVVERDEGGRALVRLDGRPFRIRLDPGPANRLAAIGWNVDPSDLAAIAEQVEKACYSVVTADAELAADRAAAQVRQFADNDGFTHELYVESSFPTDPVLESLFVCGEEANGIFGLGHLVVIVADRAKTQSFFTDVLGFGLSDRVTWPEADIFFLHCNQRHHTVALSAPALGLKPGMVHHLMLEAKSKEQVDRAFAAVKRLGYDVLMTIGQHSNDKVYSFYMMAPAGFAVELGFGGQVIGDLESWHVGFYDAPSIWGHELQ 290
                                    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         


Chain C from PDB  Type:PROTEIN  Length:289
 aligned with A5VGW5_SPHWW | A5VGW5 from UniProtKB/TrEMBL  Length:294

    Alignment length:289
                                    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         
         A5VGW5_SPHWW     2 SVKQLGYLIFECRADVLEQMVVVYQDIIGAVVERDEGGRALVRLDGRPFRIRLDPGPANRLAAIGWNVDPSDLAAIAEQVEKACYSVVTADAELAADRAAAQVRQFADNDGFTHELYVESSFPTDPVLESLFVCGEEANGIFGLGHLVVIVADRAKTQSFFTDVLGFGLSDRVTWPEADIFFLHCNQRHHTVALSAPALGLKPGMVHHLMLEAKSKEQVDRAFAAVKRLGYDVLMTIGQHSNDKVYSFYMMAPAGFAVELGFGGQVIGDLESWHVGFYDAPSIWGHELQ 290
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhhhhhhhhhhhhhh...eeee.....eeee.......eeeee....eeeeeeee.hhhhhhhhhhhhhhh....ee.hhhhhhhh.eeeeeeee.....eeeeeee.....hhhhhh.....ee..ee...eeeeee..hhhhhhhhhhhh...eeeeeeee..eeeeeee.......eeee..........eeeeeee..hhhhhhhhhhhhhhh...eeeeeeee.....eeeeee.....eeeeee......hhhhh..eee...eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vb0 C   2 SVKQLGYLIFECRADVLEQMVVVYQDIIGAVVERDEGGRALVRLDGRPFRIRLDPGPANRLAAIGWNVDPSDLAAIAEQVEKACYSVVTADAELAADRAAAQVRQFADNDGFTHELYVESSFPTDPVLESLFVCGEEANGIFGLGHLVVIVADRAKTQSFFTDVLGFGLSDRVTWPEADIFFLHCNQRHHTVALSAPALGLKPGMVHHLMLEAKSKEQVDRAFAAVKRLGYDVLMTIGQHSNDKVYSFYMMAPAGFAVELGFGGQVIGDLESWHVGFYDAPSIWGHELQ 290
                                    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         


Chain D from PDB  Type:PROTEIN  Length:289
 aligned with A5VGW5_SPHWW | A5VGW5 from UniProtKB/TrEMBL  Length:294

    Alignment length:289
                                    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         
         A5VGW5_SPHWW     2 SVKQLGYLIFECRADVLEQMVVVYQDIIGAVVERDEGGRALVRLDGRPFRIRLDPGPANRLAAIGWNVDPSDLAAIAEQVEKACYSVVTADAELAADRAAAQVRQFADNDGFTHELYVESSFPTDPVLESLFVCGEEANGIFGLGHLVVIVADRAKTQSFFTDVLGFGLSDRVTWPEADIFFLHCNQRHHTVALSAPALGLKPGMVHHLMLEAKSKEQVDRAFAAVKRLGYDVLMTIGQHSNDKVYSFYMMAPAGFAVELGFGGQVIGDLESWHVGFYDAPSIWGHELQ 290
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhhhhhhhhhhhhhh...eeee.....eeee.......eeeee....eeeeeeee.hhhhhhhhhhhhhhh....ee.hhhhhhhh.eeeeeeee.....eeeeeee.....hhhhhh.....ee..ee...eeeeee..hhhhhhhhhhhh...eeeeeeee..eeeeeee.......eeee..........eeeeeee..hhhhhhhhhhhhhhh.....eeeeee.....eeeeee.....eeeeee......hhhhh..eee...eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vb0 D   2 SVKQLGYLIFECRADVLEQMVVVYQDIIGAVVERDEGGRALVRLDGRPFRIRLDPGPANRLAAIGWNVDPSDLAAIAEQVEKACYSVVTADAELAADRAAAQVRQFADNDGFTHELYVESSFPTDPVLESLFVCGEEANGIFGLGHLVVIVADRAKTQSFFTDVLGFGLSDRVTWPEADIFFLHCNQRHHTVALSAPALGLKPGMVHHLMLEAKSKEQVDRAFAAVKRLGYDVLMTIGQHSNDKVYSFYMMAPAGFAVELGFGGQVIGDLESWHVGFYDAPSIWGHELQ 290
                                    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
   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 3VB0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VB0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VB0)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A5VGW5_SPHWW | A5VGW5)
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.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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: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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