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Title :   CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2'-CL DIHYDROXYBIPHENYL (DHB)

Authors :   S. Dai, J. T. Bolin

Date :   16 Apr 02 (Deposition) - 27 Nov 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Extradiol Dioxygenase, 2, 3-Dihydroxybiphenyl, Non-Heme Iron, Anaerobic, Pcb Biodegradation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Dai, F. H. Vaillancourt, H. Maaroufi, N. M. Drouin, D. B. Neau, V. Snieckus, J. T. Bolin, L. D. Eltis
Identification And Analysis Of A Bottleneck In Pcb Biodegradation
Nat. Struct. Biol. V. 12 934 2002
PubMed-ID: 12415290 | Reference-DOI: 10.1038/NSB866

Molecule 1 - BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE
	Chains	:	A
	EC Number	:	1.13.11.39
	Engineered	:	YES
	Expression System	:	PSEUDOMONAS PUTIDA
	Expression System Plasmid	:	PLEBD4
	Expression System Strain	:	KT2442
	Expression System Taxid	:	303
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BURKHOLDERIA XENOVORANS
	Organism Taxid	:	266265
	Other Details	:	BURKHOLDERIA SP. STRAIN LB400 HAS BEEN RECLASSIFED. PRIOR PUBLICATIONS MAY REFER TO THIS ORGANISM AS PSEUDOMONAS SP. STRAIN LB400 OR BURKHOLDERIA CEPACIA STRAIN LB400. SEE M.G.FAIN, J.D.HADDOCK, CURRENT MICROBIOL. (2001) 42:269-73
	Strain	:	LB400
	Synonym	:	23OHBP OXYGENASE, 2,3-DIHYDROXYBIPHENYL DIOXYGENASE, DHBD

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BP3	2	Ligand/Ion	2'-CHLORO-BIPHENYL-2,3-DIOL
2	FE2	2	Ligand/Ion	FE (II) ION

Biological Unit 1 (2, 32)

No.	Name	Count	Type	Full Name
1	BP3	16	Ligand/Ion	2'-CHLORO-BIPHENYL-2,3-DIOL
2	FE2	16	Ligand/Ion	FE (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:146 , HIS A:210 , GLU A:260 , BP3 A:300 , HOH A:9111	BINDING SITE FOR RESIDUE FE2 A 500
2	AC2	SOFTWARE	HIS A:189 , HOH A:9196 , HOH A:9197 , HOH A:9198 , HOH A:9199 , HOH A:9200	BINDING SITE FOR RESIDUE FE2 A 501
3	AC3	SOFTWARE	HIS A:146 , VAL A:148 , MET A:175 , PHE A:187 , HIS A:195 , HIS A:210 , HIS A:241 , ASN A:243 , TYR A:250 , GLU A:260 , FE2 A:500 , HOH A:9111 , HOH A:9112	BINDING SITE FOR RESIDUE BP3 A 300
4	AC4	SOFTWARE	PHE A:110 , PRO A:152 , PRO A:205 , LYS A:206 , HIS A:209 , GLY A:256 , GLU A:258	BINDING SITE FOR RESIDUE BP3 A 301

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

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

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

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 1LGT)

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:287
 aligned with BPHC_PARXL | P47228 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:287
                                    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 SIRSLGYMGFAVSDVAAWRSFLTQKLGLMEAGTTDNGDLFRIDSRAWRIAVQQGEVDDLAFAGYEVADAAGLAQMADKLKQAGIAVTTGDASLARRRGVTGLITFADPFGLPLEIYYGASEVFEKPFLPGAAVSGFLTGEQGLGHFVRCVPDSDKALAFYTDVLGFQLSDVIDMKMGPDVTVPAYFLHCNERHHTLAIAAFPLPKRIHHFMLEVASLDDVGFAFDRVDADGLITSTLGRHTNDHMVSFYASTPSGVEVEYGWSARTVDRSWVVVRHDSPSMWGHKSV 288
               SCOP domains d1lgta1 A:2-132 2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme)                                                              d1lgta2 A:133-288 2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme)                                                                                      SCOP domains
               CATH domains 1lgtA01 A:2-133 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                     1lgtA02 A:134-288 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.hhhhhhhhhhhh...eeeeee..eeeee.......eeeee....eeeeeeeee.hhhhhhhhhhhhhhh....ee.hhhhhhhhh..eeeeee.....eeeeee....................hhhhh..eeeee..hhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeee.......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
                 1lgt A   2 SIRSLGYMGFAVSDVAAWRSFLTQKLGLMEAGTTDNGDLFRIDSRAWRIAVQQGEVDDLAFAGYEVADAAGLAQMADKLKQAGIAVTTGDASLARRRGVTGLITFADPFGLPLEIYYGASEVFEKPFLPGAAVSGFLTGEQGLGHFVRCVPDSDKALAFYTDVLGFQLSDVIDMKMGPDVTVPAYFLHCNERHHTLAIAAFPLPKRIHHFMLEVASLDDVGFAFDRVDADGLITSTLGRHTNDHMVSFYASTPSGVEVEYGWSARTVDRSWVVVRHDSPSMWGHKSV 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

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 '\|'

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	1lgtA01	A:2-133
1b	1lgtA02	A:134-288

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

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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Biological Unit
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	1lgt
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	1.13.11.39
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	BPHC_PARXL \| P47228	:	1han 1kmy 1knd 1knf 1lkd

1han	CRYSTAL STRUCTURE OF THE BIPHENYL-CLEAVING EXTRADIOL DIOXYGENASE FROM A PCB-DEGRADING PSEUDOMONAD
1kmy	CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE COMPLEXED WITH 2,3-DIHYDROXYBIPHENYL UNDER ANAEROBIC CONDITION
1knd	CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE COMPLEXED WITH CATECHOL UNDER ANAEROBIC CONDITION
1knf	CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE COMPLEXED WITH 3-METHYL CATECHOL UNDER ANAEROBIC CONDITION
1lkd	CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2', 6'- DICL DIHYDROXYBIPHENYL (DHB)

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SS Bonds (0, 0)

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Gene Ontology (11, 11)

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