Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH 4-NITROCATECHOL
 
Authors :  M. W. Vetting, D. A. D'Argenio, L. N. Ornston, D. H. Ohlendorf
Date :  22 Mar 00  (Deposition) - 09 Aug 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (12x)
Keywords :  Beta-Sandwich, Mixed Alpha/Beta Structure, Dioxygenase, Biodegradation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. W. Vetting, D. A. D'Argenio, L. N. Ornston, D. H. Ohlendorf
Structure Of Acinetobacter Strain Adp1 Protocatechuate 3, 4-Dioxygenase At 2. 2 A Resolution: Implications For The Mechanism Of An Intradiol Dioxygenase.
Biochemistry V. 39 7943 2000
PubMed-ID: 10891075  |  Reference-DOI: 10.1021/BI000151E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
    ChainsA
    EC Number1.13.11.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificACINETOBACTER SP.
    Organism Taxid62977
    StrainADP1
 
Molecule 2 - PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
    ChainsB
    EC Number1.13.11.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificACINETOBACTER SP.
    Organism Taxid62977
    StrainADP1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
14NC1Ligand/Ion4-NITROCATECHOL
2FE1Ligand/IonFE (III) ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
14NC12Ligand/Ion4-NITROCATECHOL
2FE-1Ligand/IonFE (III) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:408 , HIS B:460 , HIS B:462 , HOH B:700 , 4NC B:999BINDING SITE FOR RESIDUE FE B 600
2AC2SOFTWARETHR A:12 , PRO A:15 , ARG A:133 , TYR B:324 , TYR B:408 , TRP B:449 , ARG B:457 , HIS B:460 , HIS B:462 , ILE B:491 , FE B:600 , HOH B:700BINDING SITE FOR RESIDUE 4NC B 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EOC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EOC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTRADIOL_DIOXYGENASPS00083 Intradiol ring-cleavage dioxygenases signature.PCXA_ACIAD55-83  1A:51-79
PCXB_ACIAD81-109  1B:380-408
Biological Unit 1 (1, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTRADIOL_DIOXYGENASPS00083 Intradiol ring-cleavage dioxygenases signature.PCXA_ACIAD55-83  12A:51-79
PCXB_ACIAD81-109  12B:380-408

(-) Exons   (0, 0)

(no "Exon" information available for 1EOC)

(-) 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:202
 aligned with PCXA_ACIAD | P20371 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:202
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207  
           PCXA_ACIAD     8 ELKETPSQTGGPYVHIGLLPKQANIEVFEHNLDNNLVQDNTQGQRIRLEGQVFDGLGLPLRDVLIEIWQADTNGVYPSQADTQGKQVDPNFLGWGRTGADFGTGFWSFNTIKPGAVPGRKGSTQAPHISLIIFARGINIGLHTRVYFDDEAEANAKDPVLNSIEWATRRQTLVAKREERDGEVVYRFDIRIQGENETVFFDI 209
               SCOP domains d1eoca_ A: Protocatechuate-3,4-dioxygenase, alpha chain                                                                                                                                                    SCOP domains
               CATH domains 1eocA00 A:4-200 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhh....................eeeeee.ee..........eeeee.........................eeeee.......eeeeee................eeeeee.......eeeeeee..hhhhhhh..hhhhh.hhhhhhh.eeeeee....eeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eoc A   4 ELKETPSQTGGPYVHIGLLPKQANIEVFEHNLDNNLVQDNTQGQRIRLEGQVFDGLGLPLRDVLIEIWQADTNGVYPSQADTQGKQVDPNFLGWGRTGADFGTGFWSFNTIKPGAVPGRKGSTQAPHISLIIFARGINIGLHTRVYFDDEAEANAKDPVLNSIEWATRRQTLVAKREERDGEVVYRFDIRIQGENETVFFDI 200
                                    13        23        33        43        53        63        73        83     ||88E        98       108       118       128       138       148       158       168       178       188       198  
                                                                                                               88A||||                                                                                                                
                                                                                                                88B|||                                                                                                                
                                                                                                                 88C||                                                                                                                
                                                                                                                  88D|                                                                                                                
                                                                                                                   88E                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with PCXB_ACIAD | P20372 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:238
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233        
           PCXB_ACIAD     4 IIWGAYAQRNTEDHPPAYAPGYKTSVLRSPKNALISIAETLSEVTAPHFSADKFGPKDNDLILNYAKDGLPIGERVIVHGYVRDQFGRPVKNALVEVWQANASGRYRHPNDQYIGAMDPNFGGCGRMLTDDNGYYVFRTIKPGPYPWRNRINEWRPAHIHFSLIADGWAQRLISQFYFEGDTLIDSCPILKTIPSEQQRRALIALEDKSNFIEADSRCYRFDITLRGRRATYFENDLT 241
               SCOP domains d1eocb_ B: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains 1eocB00 B:303-540 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhh.......hhhhh........ee...hhhhhh....hhhhh....................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee..eeeeeee..hhhhheeeeeee..hhhhhhh.hhhhh.hhhhhhh.eeee.hhhh.....eeee..eee..eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eoc B 303 IIWGAYAQRNTEDHPPAYAPGYKTSVLRSPKNALISIAETLSEVTAPHFSADKFGPKDNDLILNYAKDGLPIGERVIVHGYVRDQFGRPVKNALVEVWQANASGRYRHPNDQYIGAMDPNFGGCGRMLTDDNGYYVFRTIKPGPYPWRNRINEWRPAHIHFSLIADGWAQRLISQFYFEGDTLIDSCPILKTIPSEQQRRALIALEDKSNFIEADSRCYRFDITLRGRRATYFENDLT 540
                                   312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532        

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EOC)

(-) Gene Ontology  (14, 26)

Asymmetric Unit(hide GO term definitions)
Chain A   (PCXA_ACIAD | P20371)
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:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0018578    protocatechuate 3,4-dioxygenase activity    Catalysis of the reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate.
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:0042952    beta-ketoadipate pathway    A pathway of aromatic compound degradation by ortho-cleavage; one branch converts protocatechuate, derived from phenolic compounds, to beta-ketoadipate, and the other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates.
    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   (PCXB_ACIAD | P20372)
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:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0018578    protocatechuate 3,4-dioxygenase activity    Catalysis of the reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate.
biological process
    GO:0019619    3,4-dihydroxybenzoate catabolic process    The chemical reactions and pathways resulting in the breakdown of 3,4-dihydroxybenzoate.
    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:0042952    beta-ketoadipate pathway    A pathway of aromatic compound degradation by ortho-cleavage; one branch converts protocatechuate, derived from phenolic compounds, to beta-ketoadipate, and the other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
    4NC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1eoc)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1eoc
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PCXA_ACIAD | P20371
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  PCXB_ACIAD | P20372
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.13.11.3
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PCXA_ACIAD | P20371
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PCXB_ACIAD | P20372
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PCXA_ACIAD | P203711eo2 1eo9 1eoa 1eob 2bum 2buq 2bur 2but 2buu 2buv 2buw 2bux 2buy 2buz 2bv0
        PCXB_ACIAD | P203721eo2 1eo9 1eoa 1eob 2bum 2buq 2bur 2but 2buu 2buv 2buw 2bux 2buy 2buz 2bv0

(-) Related Entries Specified in the PDB File

1eo2 CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE AT PH 8.5
1eo9 CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE AT PH < 7.0
1eoa CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH CYANIDE
1eob CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH 3,4-DIHYDROXYBENZOATE