1HAN - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE BIPHENYL-CLEAVING EXTRADIOL DIOXYGENASE FROM A PCB-DEGRADING PSEUDOMONAD

Authors :   S. Han, J. T. Bolin

Date :   30 Aug 95 (Deposition) - 14 Nov 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Extradiol Dioxygenase, Oxidoreductase (Oxygenase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Han, L. D. Eltis, K. N. Timmis, S. W. Muchmore, J. T. Bolin
Crystal Structure Of The Biphenyl-Cleaving Extradiol Dioxygenase From A Pcb-Degrading Pseudomonad.
Science V. 270 976 1995
PubMed-ID: 7481800
(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 Gene	:	BPHC
	Expression System Plasmid	:	PLEBD4
	Expression System Taxid	:	292
	Gene	:	BPHC
	Mutation	:	YES
	Organism Scientific	:	BURKHOLDERIA XENOVORANS
	Organism Taxid	:	266265
	Other Details	:	FE(II) FORM UNDER ANAEROBIC CONDITIONS
	Other Details - Source	:	HYPEREXPRESSED IN THE PARENT STRAIN
	Strain	:	LB400
	Synonym	:	BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE, DHBD, BPHC

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	FE	2	Ligand/Ion	FE (III) ION
2	TBU	1	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	TBU	8	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:146 , HIS A:210 , GLU A:260 , HOH A:3001 , HOH A:3012	BINDING SITE FOR RESIDUE FE A 500
2	AC2	SOFTWARE	HIS A:189	BINDING SITE FOR RESIDUE FE A 501
3	AC3	SOFTWARE	PHE A:202 , HIS A:209 , TYR A:250 , PRO A:280	BINDING SITE FOR RESIDUE TBU A 600
4	FE1	AUTHOR	HIS A:146 , HIS A:210 , GLU A:260 , HOH A:3001 , HOH A:3012	ACTIVE SITE: FE(II) BINDING SITE CONSISTING IN THE FIRST SHELL OF THREE PROTEIN RESIDUES AND TWO SOLVENT SPECIES, WHICH MAY BE HOH OR OH- BUT WERE REFINED AS HOH

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

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

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

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 1HAN)

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 d1hana1 A:2-132 2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme)                                                              d1hana2 A:133-289 2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme)                                                                                       SCOP domains
               CATH domains 1hanA01 A:2-133 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                     1hanA02 A:134-288 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhh..eeeeee..eeeee......eeeeee....eeeeeeeee.hhhhhhhhhhhhhhh....eeehhhhhhhh..eeeeeeee...eeeeeee...........................eeeeee.hhhhhhhhhhhhh..eeeeeeeeee....eeeeeeee......eeeee......eeeeeeeee.hhhhhhhhhhhhhhh.eeeeeeeee....eeeeeeee...eeeeeee...........eee..eeeeeeeee. 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
                 1han 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)
	-	→ 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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

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	1hanA01	A:2-133
1b	1hanA02	A:134-288

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

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
	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
		FE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TBU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		FE1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1han)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1han
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	BPHC_PARXL \| P47228
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.13.11.39
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	BPHC_PARXL \| P47228
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	BPHC_PARXL \| P47228	:	1kmy 1knd 1knf 1lgt 1lkd

(no "Related Entries Specified in the PDB File" available for 1HAN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File