3HKP - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE DETERMINATION OF CATECHOL 1,2-DIOXYGENASE FROM RHODOCOCCUS OPACUS 1CP IN COMPLEX WITH PROTOCATECHUATE

Authors :   I. Matera, M. Ferraroni, M. Kolomytseva, F. Briganti, A. Scozzafava

Date :   25 May 09 (Deposition) - 12 Jan 10 (Release) - 26 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Beta-Sandwich, Aromatic Hydrocarbons Catabolism, Dioxygenase, Iron, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Matera, M. Ferraroni, M. Kolomytseva, L. Golovleva, A. Scozzafava, F. Briganti
Catechol 1, 2-Dioxygenase From The Gram-Positive Rhodococcus Opacus 1Cp: Quantitative Structure/Activity Relationship And The Crystal Structures Of Native Enzyme And Catechols Adducts.
J. Struct. Biol. V. 170 548 2010
PubMed-ID: 20040374 | Reference-DOI: 10.1016/J.JSB.2009.12.023

Molecule 1 - CATECHOL 1,2-DIOXYGENASE
	Chains	:	A
	EC Number	:	1.13.11.1
	Organism Common	:	NOCARDIA OPACA
	Organism Scientific	:	RHODOCOCCUS OPACUS
	Organism Taxid	:	37919
	Other Details	:	GROWN ON BENZOATE
	Strain	:	1CP
	Synonym	:	1,2-CTD

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	6PL	1	Ligand/Ion	(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
2	DHB	1	Ligand/Ion	3,4-DIHYDROXYBENZOIC ACID
3	FE	1	Ligand/Ion	FE (III) ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	6PL	2	Ligand/Ion	(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
2	DHB	2	Ligand/Ion	3,4-DIHYDROXYBENZOIC ACID
3	FE	-1	Ligand/Ion	FE (III) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:162 , HIS A:220 , HIS A:222 , DHB A:282	BINDING SITE FOR RESIDUE FE A 281
2	AC2	SOFTWARE	LEU A:77 , ASP A:80 , VAL A:81 , ILE A:102 , PRO A:105 , TYR A:106 , TYR A:162 , TYR A:196 , ARG A:217 , HIS A:220 , HIS A:222 , FE A:281 , HOH A:333	BINDING SITE FOR RESIDUE DHB A 282
3	AC3	SOFTWARE	ALA A:25 , THR A:26 , THR A:29 , ILE A:37 , LEU A:45 , ILE A:49 , GLU A:58 , VAL A:61 , PHE A:62 , TRP A:65 , GLN A:206 , PHE A:207	BINDING SITE FOR RESIDUE 6PL A 283

(no "SS Bond" information available for 3HKP)

(no "Cis Peptide Bond" information available for 3HKP)

(no "SAP(SNP)/Variant" information available for 3HKP)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTRADIOL_DIOXYGENAS	PS00083	Intradiol ring-cleavage dioxygenases signature.	CATA_RHOOP	124-152	1	A:134-162

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTRADIOL_DIOXYGENAS	PS00083	Intradiol ring-cleavage dioxygenases signature.	CATA_RHOOP	124-152	2	A:134-162

(no "Exon" information available for 3HKP)

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:256
 aligned with CATA_RHOOP | P95607 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:256
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264      
           CATA_RHOOP    15 ATADTSPERLAAIAKDALGALNDVILKHGVTYPEYRVFKQWLIDVGEGGEWPLFLDVFIEHSVEEVLARSRKGTMGSIEGPYYIENSPELPSKCTLPMREEDEKITPLVFSGQVTDLDGNGLAGAKVELWHADNDGYYSQFAPHLPEWNLRGTIIADEEGRYEITTIQPAPYQIPTDGPTGQFIEAQNGHPWRPAHLHLIVSAPGKESVTTQLYFKGGEWIDSDVASATKPELILDPKTGDDGKNYVTYNFVLDPA 270
               SCOP domains d3hkpa_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...................ee..eee...hhhhhh..eeeeeeeee..........eeeeee...................eeeee.....eeeeeee....ee....hhhhhhhhh.....ee...eeeeee......eeeeeee..............hhh.ee..ee.....eeee..ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hkp A  25 ATADTSPERLAAIAKDALGALNDVILKHGVTYPEYRVFKQWLIDVGEGGEWPLFLDVFIEHSVEEVLARSRKGTMGSIEGPYYIENSPELPSKCTDPMREEDEKITPLVFSGQVTDLDGNGLAGAKVELWHADNDGYYSQFAPHLPEWNLRGTIIADEEGRYEITTIQPAPYQIPTDGPTGQFIEAQNGHPWRPAHLHLIVSAPGKESVTTQLYFKGGEWIDSDVASATKPELILDPKTGDDGKNYVTYNFVLDPA 280
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Prealbumin-like (433)

Superfamily: Aromatic compound dioxygenase (111)

Family: automated matches (11)

Protein domain: automated matches (11)

Rhodococcus opacus [TaxId: 37919] (11)

d3hkpa_

(no "CATH Domain" information available for 3HKP)

(no "Pfam Domain" information available for 3HKP)

Asymmetric Unit(hide GO term definitions)

Chain A (CATA_RHOOP | P95607)

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:0018576	catechol 1,2-dioxygenase activity	Catalysis of the reaction: catechol + O2 = cis,cis-muconate.
	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.
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:0009712	catechol-containing compound metabolic process	The chemical reactions and pathways involving a compound containing a pyrocatechol (1,2-benzenediol) nucleus or substituent.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3hkp)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3hkp
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	1.13.11.1
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UniProtKB/Swiss-Prot
	CATA_RHOOP \| P95607	:	3hgi 3hhx 3hhy 3hj8 3hjq 3hjs 3i4v 3i4y 3i51

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Ligands, Modified Residues, Ions (3, 3)

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