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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE PROTOCATECHUATE 3,4-DIOXYGENASE FROM ACINETOBACTER SP. ADP1
 
Authors :  M. W. Vetting, M. P. Valley, D. A. D'Argenio, L. N. Ornston, J. D. Lipscom D. H. Ohlendorf
Date :  14 Jun 05  (Deposition) - 05 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (12x)
Keywords :  Oxidoreductase, Aromatic Degradation, Non-Heme Iron, Beta-Sandwich, Mixed Alpha/Beta Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. K. Brown, M. W. Vetting, C. A. Earhart, D. H. Ohlendorf
Biophysical Analyses Of Designed And Selected Mutants Of Protocatechuate 3, 4-Dioxygenase
Annu. Rev. Microbiol. V. 58 555 2004
PubMed-ID: 15487948  |  Reference-DOI: 10.1146/ANNUREV.MICRO.57.030502.090927
(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 StrainB86DE3
    Expression System Taxid562
    Expression System VectorPUC18-DERIVED PLASMID
    Organism ScientificACINETOBACTER SP.
    Organism Taxid62977
    StrainADP1
    SynonymPROTOCATECHUATE 3,4-DIOXYGENASE, 3,4-PCD
 
Molecule 2 - PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
    ChainsB
    EC Number1.13.11.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainB86DE3
    Expression System Taxid562
    Expression System VectorPUC18-DERIVED PLASMID
    Organism ScientificACINETOBACTER SP.
    Organism Taxid62977
    StrainADP1
    SynonymPROTOCATECHUATE 3,4-DIOXYGENASE, 3,4-PCD

 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
1FE1Ligand/IonFE (III) ION
2OH1Ligand/IonHYDROXIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2OH-1Ligand/IonHYDROXIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:408 , TYR B:447 , HIS B:460 , HIS B:462 , OH B:1542BINDING SITE FOR RESIDUE FE B1541
2AC2SOFTWAREPRO A:15 , HOH A:2009 , TYR B:408 , TYR B:447 , HIS B:462 , FE B:1541 , HOH B:2092BINDING SITE FOR RESIDUE OH B1542

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 2BUM)

(-) 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 d2buma_ A: automated matches                                                                                                                                                                               SCOP domains
               CATH domains 2bumA00 A:4-200 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhh....................eeeeee.ee..........eeeee.........................eeeee.......eeeeee................eeeeee.......eeeeeee..hhhhhh.hhhhhh..hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bum 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 d2bumb_ B: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains 2bumB00 B:303-540 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhh.......hhhhhh.......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
                 2bum 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 2BUM)

(-) 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCXA_ACIAD | P203711eo2 1eo9 1eoa 1eob 1eoc 2buq 2bur 2but 2buu 2buv 2buw 2bux 2buy 2buz 2bv0
        PCXB_ACIAD | P203721eo2 1eo9 1eoa 1eob 1eoc 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
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
1eoc CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4- DIOXYGENASE IN COMPLEX WITH 4-NITROCATECHOL
2buq CRYSTAL STRUCTURE OF WILD-TYPE PROTOCATECHUATE 3,4-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 IN COMPLEX WITH CATECHOL
2bur CRYSTAL STRUCTURE OF WILD-TYPE PROTOCATECHUATE 3,4-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 IN COMPLEX WITH 4-HYDROXYBENZOATE
2but CRYSTAL STRUCTURE OF PROTOCATECHUATE 3,4- DIOXYGENASE FROM ACINETOBACTER SP. ADP1 MUTANT R457S - APO
2buu CRYSTAL STRUCTURE OF PROTOCATECHUATE 3,4- DIOXYGENASE FROM ACINETOBACTER SP. ADP1 MUTANT R457S IN COMPLEX WITH 4-NITROCATECHOL
2buv CRYSTAL STRUCTURE OF PROTOCATECHUATE 3,4- DIOXYGENASE FROM ACINETOBACTER SP. ADP1 MUTANT R457S IN COMPLEX WITH PROTOCATECHUATE
2buw CRYSTAL STRUCTURE OF PROTOCATECHUATE 3,4- DIOXYGENASE FROM ACINETOBACTER SP. ADP1 MUTANT R457S IN COMPLEX WITH 4-HYDROXYBENZOATE
2bux CRYSTAL STRUCTURE OF PROTOCATECHUATE 3,4- DIOXYGENASE FROM ACINETOBACTER SP. ADP1 MUTANT R133H
2buy CRYSTAL STRUCTURE OF PROTOCATECHUATE 3,4- DIOXYGENASE FROM ACINETOBACTER SP. ADP1 MUTANT R133H IN COMPLEX WITH CATECHOL