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(-) Description

Title :  THE HIS145ALA MUTANT OF 2,3-DIHYDROXYBIPHENYL DIOXYGENASE IN COMPLEX WITH 2,3-DIHYDROXYBIPHENYL
 
Authors :  N. Sato, Y. Uragami, T. Nishizaki, Y. Takahashi, G. Sazaki, K. Sugimoto T. Nonaka, E. Masai, M. Fukuda, T. Senda
Date :  29 Jan 02  (Deposition) - 29 Jan 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  B
Biol. Unit 1:  B  (8x)
Keywords :  Four Time Repetitions Of The Beta-Alpha-Beta-Beta-Beta Motif, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Sato, Y. Uragami, T. Nishizaki, Y. Takahashi, G. Sazaki, K. Sugimoto, T. Nonaka, E. Masai, M. Fukuda, T. Senda
Crystal Structures Of The Reaction Intermediate And Its Homologue Of An Extradiol-Cleaving Catecholic Dioxygenase
J. Mol. Biol. V. 321 621 2002
PubMed-ID: 12206778  |  Reference-DOI: 10.1016/S0022-2836(02)00673-3

(-) Compounds

Molecule 1 - 2,3-DIHYDROXYBIPHENYL DIOXYGENASE
    Chains: B
    EC Number: 1.13.11.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 307
    Strain: KKS102
    Synonym: BPHC, BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1BPY1Ligand/IonBIPHENYL-2,3-DIOL
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1BPY8Ligand/IonBIPHENYL-2,3-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE B:186 , HIS B:194 , HIS B:208 , HIS B:209 , HIS B:240 , ASN B:242 , ASP B:243 , TYR B:249 , GLU B:260BINDING SITE FOR RESIDUE BPY B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VOCPS51819 Vicinal oxygen chelate (VOC) domain profile.BPHC_PSES15-119
143-265		  2B:4-118
B:142-264
2EXTRADIOL_DIOXYGENASPS00082 Extradiol ring-cleavage dioxygenases signature.BPHC_PSES1239-259  1B:238-258
Biological Unit 1 (2, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VOCPS51819 Vicinal oxygen chelate (VOC) domain profile.BPHC_PSES15-119
143-265		  16B:4-118
B:142-264
2EXTRADIOL_DIOXYGENASPS00082 Extradiol ring-cleavage dioxygenases signature.BPHC_PSES1239-259  8B:238-258

(-) Exons   (0, 0)

(no "Exon" information available for 1KWC)

(-) 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 B from PDB  Type:PROTEIN  Length:288
 aligned with BPHC_PSES1 | P17297 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:288
                                    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        
           BPHC_PSES1     2 SIERLGYLGFAVKDVPAWDHFLTKSVGLMAAGSAGDAALYRADQRAWRIAVQPGELDDLAYAGLEVDDAAALERMADKLRQAGVAFTRGDEALMQQRKVMGLLCLQDPFGLPLEIYYGPAEIFHEPFLPSAPVSGFVTGDQGIGHFVRCVPDTAKAMAFYTEVLGFVLSDIIDIQMGPETSVPAHFLHCNGRHHTIALAAFPIPKRIHHFMLQANTIDDVGYAFDRLDAAGRITSLLGRHTNDQTLSFYADTPSPMIEVEFGWGPRTVDSSWTVARHSRTAMWGHKSV 289
               SCOP domains d1kwcb1 B:1-132 2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme)                                                               d1kwcb2 B:133-288 2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme)                                                                                      SCOP domains
               CATH domains 1kwcB01 B:1-132 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                     1kwcB02 B:133-286 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                         -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-1kwcB01 B:142-261                                                                                            --------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhhh...eeeeee..eeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhhh...ee.hhhhhhhhh..eeeeee.....eeeeee....................hhhhh..eeeee..hhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeee.......eeee.......eeeeeee..hhhhhhhhhhhhhhh.......eee.....eeeeee......eeeeee...........eee...eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---VOC  PDB: B:4-118 UniProt: 5-119                                                                                   -----------------------VOC  PDB: B:142-264 UniProt: 143-265                                                                                       ------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EXTRADIOL_DIOXYGENAS ------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kwc B   1 SIERLGYLGFAVKDVPAWDHFLTKSVGLMAAGSAGDAALYRADQRAWRIAVQPGELDDLAYAGLEVDDAAALERMADKLRQAGVAFTRGDEALMQQRKVMGLLCLQDPFGLPLEIYYGPAEIFHEPFLPSAPVSGFVTGDQGIGAFVRCVPDTAKAMAFYTEVLGFVLSDIIDIQMGPETSVPAHFLHCNGRHHTIALAAFPIPKRIHHFMLQANTIDDVGYAFDRLDAAGRITSLLGRHTNDQTLSFYADTPSPMIEVEFGWGPRTVDSSWTVARHSRTAMWGHKSV 288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Glyoxalase (58)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain B   (BPHC_PSES1 | P17297)
molecular function
    GO:0018583    biphenyl-2,3-diol 1,2-dioxygenase activity    Catalysis of the reaction: biphenyl-2,3-diol + O2 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate + H2O.
    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: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.
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.
    GO:0042178    xenobiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.

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  1.13.11.39
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 Related Entries

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

UniProtKB/Swiss-Prot
        BPHC_PSES1 | P17297: 1dhy 1eil 1eiq 1eir 1kw3 1kw6 1kw8 1kw9 1kwb

(-) Related Entries Specified in the PDB File

1kw3 1KW3 CONTAINS THE SAME PROTEIN AT 1.45 A RESOLUTION.
1kw6 1KW6 CONTAINS THE SAME PROTEIN COMPLEXED WITH 2,3- DIHYDROXYBIPHENYL AT 1.45 A RESOLUTION.
1kw8 1KW8 CONTAINS THE SAME PROTEIN COMPLEXED WITH 2,3- DIHYDROXYBIPHENYL-NO.
1kw9 1KW9 CONTAINS THE SAME PROTEIN COMPLEXED WITH 2,3- DIHYDROXYBIPHENYL AT 2.0 A RESOLUTION.
1kwb 1KWB CONTAINS THE SAME PROTEIN, H145A MUTANT.