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(-) Description

Title :  ANAEROBIC CRYSTAL STRUCTURE ANALYSIS OF 1,2-DIHYDROXYNAPHTHALENE DIOXYGENASE FROM PSEUDOMONAS SP. STRAIN C18 COMPLEXED WITH 3,4-DIHYDROXYBIPHENYL
 
Authors :  D. B. Neau, M. S. Kelker, C. L. Colbert, J. T. Bolin
Date :  10 Mar 07  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Extradiol Dioxygenase, Protein Substrate Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. B. Neau, M. S. Kelker, H. Maaroufi, C. L. Colbert, L. D. Eltis, J. T. Bolin
Structural Explanation For Success And Failure In The Enzymatic Ring-Cleavage Of 3, 4 Dihydroxybiphenyl And Relate Pcb Metabolites
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 1,2-DIHYDROXYNAPHTHALENE DIOXYGENASE
    Chains: A
    EC Number: 1.13.11.-
    Engineered: YES
    Expression System: PSEUDOMONAS PUTIDA
    Expression System Plasmid: PHMPVDG
    Expression System Strain: KT2442
    Expression System Taxid: 303
    Expression System Vector Type: PLASMID
    Gene: DOXG
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 69011
    Strain: C18

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (8x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1BP73Ligand/Ion1,1'-BIPHENYL-3,4-DIOL
2FE21Ligand/IonFE (II) ION
3GOL1Ligand/IonGLYCEROL
4MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 40)
No.NameCountTypeFull Name
1BP724Ligand/Ion1,1'-BIPHENYL-3,4-DIOL
2FE28Ligand/IonFE (II) ION
3GOL8Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:152 , HIS A:215 , TYR A:256 , GLU A:266 , BP7 A:400BINDING SITE FOR RESIDUE FE2 A 399
2AC2SOFTWAREGLU A:177 , HOH A:903 , HOH A:904 , HOH A:905 , HOH A:906 , HOH A:907BINDING SITE FOR RESIDUE MG A 398
3AC3SOFTWAREHIS A:152 , TYR A:178 , LEU A:190 , PHE A:192 , HIS A:200 , HIS A:215 , HIS A:247 , ASN A:249 , TYR A:256 , GLU A:266 , ASP A:284 , FE2 A:399BINDING SITE FOR RESIDUE BP7 A 400
4AC4SOFTWAREILE A:154 , PHE A:192 , PHE A:204 , MET A:207 , ASN A:214 , HOH A:1066 , HOH A:1144BINDING SITE FOR RESIDUE BP7 A 401
5AC5SOFTWAREGLY A:171 , ARG A:173 , HIS A:194 , CYS A:195 , ASN A:196 , ALA A:197 , ASP A:276 , HOH A:1174BINDING SITE FOR RESIDUE BP7 A 402
6AC6SOFTWARETYR A:12 , TRP A:51 , HIS A:52 , HIS A:53 , ARG A:103 , MET A:104 , PRO A:125 , ARG A:126BINDING SITE FOR RESIDUE GOL A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EI0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EI0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EI0)

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VOCPS51819 Vicinal oxygen chelate (VOC) domain profile.NAHC_PSEU89-124
149-270		  2A:9-124
A:149-270
2EXTRADIOL_DIOXYGENASPS00082 Extradiol ring-cleavage dioxygenases signature.NAHC_PSEU8245-266  1A:245-266
Biological Unit 1 (2, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VOCPS51819 Vicinal oxygen chelate (VOC) domain profile.NAHC_PSEU89-124
149-270		  16A:9-124
A:149-270
2EXTRADIOL_DIOXYGENASPS00082 Extradiol ring-cleavage dioxygenases signature.NAHC_PSEU8245-266  8A:245-266

(-) Exons   (0, 0)

(no "Exon" information available for 2EI0)

(-) 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:286
 aligned with NAHC_PSEU8 | P0A108 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:291
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294 
           NAHC_PSEU8     5 AAVIELGYMGISVKDPDAWKSFATDMLGLQVLDEGEKDRFYLRMDYWHHRIVVHHNGQDDLEYLGWRVAGKPEFEALGQKLIDAGYKIRICDKVEAQERMVLGLMKTEDPGGNPTEIFWGPRIDMSNPFHPGRPLHGKFVTGDQGLGHCIVRQTDVAEAHKFYSLLGFRGDVEYRIPLPNGMTAELSFMHCNARDHSIAFGAMPAAKRLNHLMLEYTHMEDLGYTHQQFVKNEIDIALQLGIHANDKALTFYGATPSGWLIEPGWRGATAIDEAEYYVGDIFGHGVEATGY 295
               SCOP domains d2ei0a1 A:5-137 automated matches                                                                                                    d2ei0a2 A:138-295 automated matches                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee..hhhhhhhhhhhh...eee......eeeee.......eeee.....eeeeeeeee.hhhhhhhhhhhhhhh....ee.hhhhhhhhheeeeeeee.....eeeeeeee...................hhhhh..eeee...hhhhhhhhhhhh.....eeeee.-----.eeeeee........eee........eeeeeeee.hhhhhhhhhhhhhhh...eeeeeee......eeeeee.....eeeeee................ee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----VOC  PDB: A:9-124 UniProt: 9-124                                                                                    ------------------------VOC  PDB: A:149-270 UniProt: 149-270                                                                                      ------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EXTRADIOL_DIOXYGENAS  ----------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ei0 A   5 AAVIELGYMGISVKDPDAWKSFATDMLGLQVLDEGEKDRFYLRMDYWHHRIVVHHNGQDDLEYLGWRVAGKPEFEALGQKLIDAGYKIRICDKVEAQERMVLGLMKTEDPGGNPTEIFWGPRIDMSNPFHPGRPLHGKFVTGDQGLGHCIVRQTDVAEAHKFYSLLGFRGDVEYRIP-----TAELSFMHCNARDHSIAFGAMPAAKRLNHLMLEYTHMEDLGYTHQQFVKNEIDIALQLGIHANDKALTFYGATPSGWLIEPGWRGATAIDEAEYYVGDIFGHGVEATGY 295
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174      |  -  |    194       204       214       224       234       244       254       264       274       284       294 
                                                                                                                                                                                                          181   187
   Legend:   → Mismatch (orange background)
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    → 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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EI0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EI0)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (NAHC_PSEU8 | P0A108)
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.
    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: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:1901170    naphthalene catabolic process    The chemical reactions and pathways resulting in the breakdown of naphthalene.
    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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        NAHC_PSEU8 | P0A108: 2ehz 2ei1 2ei2 2ei3

(-) Related Entries Specified in the PDB File

2ehz 2ei1 2ei2 2ei3