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Title :   CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE COMPLEXED WITH CATECHOL UNDER ANAEROBIC CONDITION

Authors :   S. Han, J. T. Bolin

Date :   18 Dec 01 (Deposition) - 27 Mar 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (8x)

Keywords :   Dioxygenase, 2, 3-Dihydroxybiphenyl, Catechol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. H. Vaillancourt, S. Han, P. D. Fortin, J. T. Bolin, L. D. Eltis
Molecular Basis For The Stabilization And Inhibition Of 2, 3-Dihydroxybiphenyl 1, 2-Dioxygenase By T-Butanol.
J. Biol. Chem. V. 273 34887 1998
PubMed-ID: 9857017 | Reference-DOI: 10.1074/JBC.273.52.34887
(for further references see the PDB file header)

Molecule 1 - 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
	Chains	:	A
	EC Number	:	1.13.11.39
	Engineered	:	YES
	Expression System	:	BURKHOLDERIA CEPACIA
	Expression System Plasmid	:	PLEBD4
	Expression System Taxid	:	292
	Expression System Vector Type	:	PLASMID
	Gene	:	BPHC
	Organism Scientific	:	BURKHOLDERIA XENOVORANS
	Organism Taxid	:	266265
	Other Details	:	HYPEREXPRESSED IN THE PARENT STRAIN (THIS ORGANISM HAS BEEN RECLASSIFIED. PRIOR PUBLICATIONS MAY REFER TO THIS SOURCE AS PSEUDOMONAS SP. STRAIN LB400.)
	Strain	:	LB400
	Synonym	:	BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE, DHBD

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CAQ	1	Ligand/Ion	CATECHOL
2	FE2	2	Ligand/Ion	FE (II) ION
3	TBU	2	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Biological Unit 1 (3, 40)

No.	Name	Count	Type	Full Name
1	CAQ	8	Ligand/Ion	CATECHOL
2	FE2	16	Ligand/Ion	FE (II) ION
3	TBU	16	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:146 , HIS A:210 , GLU A:260 , CAQ A:301 , HOH A:3001 , HOH A:3012 , HOH A:9001	BINDING SITE FOR RESIDUE FE2 A 500
2	AC2	SOFTWARE	HIS A:189	BINDING SITE FOR RESIDUE FE2 A 501
3	AC3	SOFTWARE	HIS A:146 , PHE A:187 , HIS A:195 , HIS A:210 , HIS A:241 , ASN A:243 , ASP A:244 , TYR A:250 , GLU A:260 , FE2 A:500 , HOH A:3001 , HOH A:3012 , HOH A:9001 , HOH A:9002	BINDING SITE FOR RESIDUE CAQ A 301
4	AC4	SOFTWARE	SER A:236 , TYR A:250 , ARG A:289 , TBU A:600	BINDING SITE FOR RESIDUE TBU A 601
5	AC5	SOFTWARE	PHE A:202 , TYR A:250 , PRO A:280 , TBU A:601	BINDING SITE FOR RESIDUE TBU A 600

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

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

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

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	BPHC_PARXL	5-119 143-264	2	A:5-119 A:143-264
2	EXTRADIOL_DIOXYGENAS	PS00082	Extradiol ring-cleavage dioxygenases signature.	BPHC_PARXL	239-260	1	A:239-260

Biological Unit 1 (2, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	BPHC_PARXL	5-119 143-264	16	A:5-119 A:143-264
2	EXTRADIOL_DIOXYGENAS	PS00082	Extradiol ring-cleavage dioxygenases signature.	BPHC_PARXL	239-260	8	A:239-260

(no "Exon" information available for 1KND)

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:288
 aligned with BPHC_PARXL | P47228 from UniProtKB/Swiss-Prot  Length:298

    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_PARXL     2 SIRSLGYMGFAVSDVAAWRSFLTQKLGLMEAGTTDNGDLFRIDSRAWRIAVQQGEVDDLAFAGYEVADAAGLAQMADKLKQAGIAVTTGDASLARRRGVTGLITFADPFGLPLEIYYGASEVFEKPFLPGAAVSGFLTGEQGLGHFVRCVPDSDKALAFYTDVLGFQLSDVIDMKMGPDVTVPAYFLHCNERHHTLAIAAFPLPKRIHHFMLEVASLDDVGFAFDRVDADGLITSTLGRHTNDHMVSFYASTPSGVEVEYGWSARTVDRSWVVVRHDSPSMWGHKSVR 289
               SCOP domains d1knda1 A:2-132 2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme)                                                              d1knda2 A:133-289 2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme)                                                                                       SCOP domains
               CATH domains 1kndA01 A:2-133 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                     1kndA02 A:134-288 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhhh...eeeeee..eeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh....ee.hhhhhhhhh..eeeeee.....eeeeee....................hhhhh..eeeee..hhhhhhhhhhhh...eeeeeeeee.....eeeeeeee.......eeee.......eeeeeee..hhhhhhhhhhhhhh...eeeeeeee.....eeeeee.....eeeeee...........eee...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---VOC  PDB: A:5-119 UniProt: 5-119                                                                                   -----------------------VOC  PDB: A:143-264 UniProt: 143-264                                                                                      ------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EXTRADIOL_DIOXYGENAS  ----------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1knd A   2 SIRSLGYMGFAVSDVAAWRSFLTQKLGLMEAGTTDNGDLFRIDSRAWRIAVQQGEVDDLAFAGYEVADAAGLAQMADKLKQAGIAVTTGDASLARRRGVTGLITFADPFGLPLEIYYGASEVFEKPFLPGAAVSGFLTGEQGLGHFVRCVPDSDKALAFYTDVLGFQLSDVIDMKMGPDVTVPAYFLHCNERHHTLAIAAFPLPKRIHHFMLEVASLDDVGFAFDRVDADGLITSTLGRHTNDHMVSFYASTPSGVEVEYGWSARTVDRSWVVVRHDSPSMWGHKSVR 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

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 (113)

Homologous Superfamily: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 (106)

Burkholderia xenovorans lb400. Organism_taxid: 266265. Strain: lb400. (6)

1a	1kndA01	A:2-133
1b	1kndA02	A:134-288

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

Asymmetric Unit(hide GO term definitions)

Chain A (BPHC_PARXL | P47228)

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.

Asymmetric Unit
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	BPHC_PARXL \| P47228	:	1han 1kmy 1knf 1lgt 1lkd

1han	1HAN IS THE SAME PROTEIN WITHOUT SUBSTRATE.
1kmy	1KMY IS THE CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2- DIOXYGENASE COMPLEXED WITH 2,3-DIHYDROXYBIPHENYL UNDER ANAEROBIC CONDITION.
1knf	1KNF IS THE CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2- DIOXYGENASE COMPLEXED WITH 3-METHYL CATECHOL UNDER ANAEROBIC CONDITION.

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