3O32 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 4-CHLOROCATECHOL DIOXYGENASE FROM RHODOCOCCUS OPACUS 1CP IN COMPLEX WITH 3,5-DICHLOROCATECHOL

Authors :   M. Ferraroni, F. Briganti, M. Kolomytseva, L. Golovleva

Date :   23 Jul 10 (Deposition) - 10 Aug 11 (Release) - 19 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

Chains :   Asym./Biol. Unit : A,B

Keywords :   Beta Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Ferraroni, M. Kolomytseva, A. Scozzafava, L. Golovleva, F. Briganti
X-Ray Structures Of 4-Chlorocatechol 1, 2-Dioxygenase Adduct With Substituted Catechols: New Perspectives In The Molecular Basis Of Intradiol Ring Cleaving Dioxygenases Specificity.
J. Struct. Biol. V. 181 274 2013
PubMed-ID: 23261399 | Reference-DOI: 10.1016/J.JSB.2012.11.007

Molecule 1 - CHLOROCATECHOL 1,2-DIOXYGENASE
	Chains	:	A, B
	EC Number	:	1.13.11.-
	Organism Common	:	NOCARDIA OPACA
	Organism Scientific	:	RHODOCOCCUS OPACUS
	Organism Taxid	:	37919
	Strain	:	1CP

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	35C	1	Ligand/Ion	3,5-DICHLOROBENZENE-1,2-DIOL
2	FE	2	Ligand/Ion	FE (III) ION
3	MYY	2	Ligand/Ion	(2R)-3-(PHOSPHONOOXY)-2-(TETRADECANOYLOXY)PROPYLPALMITATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:134 , HIS A:194 , HIS A:196 , 35C A:258	BINDING SITE FOR RESIDUE FE A 300
2	AC2	SOFTWARE	LEU A:49 , ASP A:52 , ALA A:53 , GLY A:76 , PRO A:77 , TYR A:134 , TYR A:169 , ARG A:191 , HIS A:194 , HIS A:196 , CYS A:224 , FE A:300	BINDING SITE FOR RESIDUE 35C A 258
3	AC3	SOFTWARE	THR A:33 , TYR A:37 , TYR A:184 , VAL B:6 , LEU B:9 , PHE B:13 , MYY B:304	BINDING SITE FOR RESIDUE MYY A 303
4	AC4	SOFTWARE	HIS B:194 , HIS B:196	BINDING SITE FOR RESIDUE FE B 301
5	AC5	SOFTWARE	VAL A:6 , LEU A:9 , PHE A:13 , MYY A:303 , ILE B:34 , TYR B:37 , TRP B:50 , TYR B:184	BINDING SITE FOR RESIDUE MYY B 304

(no "SS Bond" information available for 3O32)

(no "Cis Peptide Bond" information available for 3O32)

(no "SAP(SNP)/Variant" information available for 3O32)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTRADIOL_DIOXYGENAS	PS00083	Intradiol ring-cleavage dioxygenases signature.	CLCA_RHOOP	106-134	2	A:106-134 B:106-134

(no "Exon" information available for 3O32)

Asymmetric/Biological 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 CLCA_RHOOP | O67987 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:256
                                    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      
           CLCA_RHOOP     2 ANTRVIELFDEFTDLIRDFIVRHEITTPEYETIMQYMISVGEAGEWPLWLDAFFETTVDSVSYGKGNWTSSAIQGPFFKEGAPLLTGKPATLPMRADEPGDRMRFTGSVRDTSGTPITGAVIDVWHSTNDGNYSFFSPALPDQYLLRGRVVPAEDGSIEFHSIRPVPYEIPKAGPTGQLMNSYLGRHSWRPAHIHIRITADGYRPLITQLYFEGDPYLDSDSCSAVKSELVLPVNKIDIDGETWQLVDFNFILQHN 257
               SCOP domains d3o32a_ A: Chlorocatechol 1,2-dioxygenase                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......................................eeeeeeeeee.........eeeee.....................eeee......eeeeeee....ee....hhhhhhhhh......ee..eeeeeee......eeeeeee....hhhhh.....hhh.ee..eeee....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o32 A   2 ANTRVIELFDEFTDLIRDFIVRHEITTPEYETIMQYMISVGEAGEWPLWLDAFFETTVDSVSYGKGNWTSSAIQGPFFKEGAPLLTGKPATLPMRADEPGDRMRFTGSVRDTSGTPITGAVIDVWHSTNDGNYSFFSPALPDQYLLRGRVVPAEDGSIEFHSIRPVPYEIPKAGPTGQLMNSYLGRHSWRPAHIHIRITADGYRPLITQLYFEGDPYLDSDSCSAVKSELVLPVNKIDIDGETWQLVDFNFILQHN 257
                                    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

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with CLCA_RHOOP | O67987 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:255
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252     
           CLCA_RHOOP     3 NTRVIELFDEFTDLIRDFIVRHEITTPEYETIMQYMISVGEAGEWPLWLDAFFETTVDSVSYGKGNWTSSAIQGPFFKEGAPLLTGKPATLPMRADEPGDRMRFTGSVRDTSGTPITGAVIDVWHSTNDGNYSFFSPALPDQYLLRGRVVPAEDGSIEFHSIRPVPYEIPKAGPTGQLMNSYLGRHSWRPAHIHIRITADGYRPLITQLYFEGDPYLDSDSCSAVKSELVLPVNKIDIDGETWQLVDFNFILQHN 257
               SCOP domains d3o32b_ B: Chlorocatechol 1,2-dioxygenase                                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......................................eeeeeeeee..........eeeee.....................eeee.......eeeeee....ee....hhhhhhhhh......ee..eeeeeee......eeeeeee....hhhhh.........ee..eeeee..eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o32 B   3 NTRVIELFDEFTDLIRDFIVRHEITTPEYETIMQYMISVGEAGEWPLWLDAFFETTVDSVSYGKGNWTSSAIQGPFFKEGAPLLTGKPATLPMRADEPGDRMRFTGSVRDTSGTPITGAVIDVWHSTNDGNYSFFSPALPDQYLLRGRVVPAEDGSIEFHSIRPVPYEIPKAGPTGQLMNSYLGRHSWRPAHIHIRITADGYRPLITQLYFEGDPYLDSDSCSAVKSELVLPVNKIDIDGETWQLVDFNFILQHN 257
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Prealbumin-like (433)

Superfamily: Aromatic compound dioxygenase (111)

Family: Aromatic compound dioxygenase (100)

Protein domain: Chlorocatechol 1,2-dioxygenase (5)

Rhodococcus opacus [TaxId: 37919] (5)

1a	d3o32a_	A:
1b	d3o32b_	B:

(no "CATH Domain" information available for 3O32)

(no "Pfam Domain" information available for 3O32)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CLCA_RHOOP | O67987)

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:0018575	chlorocatechol 1,2-dioxygenase activity	Catalysis of the reaction: 3,6-dichlorocatechol + O2 = 2 H+ + 2,5-dichloro-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/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3o32)

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	3o32
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	1.13.11.-
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	CLCA_RHOOP \| O67987	:	1s9a 3o5u 3o6j 3o6r

3o5u	CRYSTAL STRUCTURE OF 4-CHLOROCATECHOL DIOXYGENASE FROM RHODOCOCCUS OPACUS 1CP IN COMPLEX WITH PROTOCATECHUATE
3o6j
3o6r

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (13, 13)

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