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Title :   STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA

Authors :   M. W. Vetting, D. H. Ohlendorf

Date :   11 Dec 99 (Deposition) - 23 May 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Metalloprotein, Dioxygenase, Aromatic Compound Degradation, Mixed Alpha Helix/ Beta Strand, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. W. Vetting, D. H. Ohlendorf
The 1. 8 A Crystal Structure Of Catechol 1, 2-Dioxygenase Reveals A Novel Hydrophobic Helical Zipper As A Subunit Linker.
Structure Fold. Des. V. 8 429 2000
PubMed-ID: 10801478 | Reference-DOI: 10.1016/S0969-2126(00)00122-2
(for further references see the PDB file header)

Molecule 1 - CATECHOL 1,2-DIOXYGENASE
	Chains	:	A, B
	EC Number	:	1.13.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ACINETOBACTER SP.
	Organism Taxid	:	62977
	Strain	:	ADP1
	Synonym	:	1,2-CTD

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	FE	2	Ligand/Ion	FE (III) ION
2	LIO	2	Ligand/Ion	[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:164 , TYR A:200 , HIS A:224 , HIS A:226 , HOH A:501	BINDING SITE FOR RESIDUE FE A 400
2	AC2	SOFTWARE	TYR B:164 , TYR B:200 , ARG B:221 , HIS B:224 , HIS B:226 , HOH B:503	BINDING SITE FOR RESIDUE FE B 400
3	AC3	SOFTWARE	ASN A:27 , GLU B:54 , TYR B:61 , HOH B:674	BINDING SITE FOR RESIDUE LIO B 999
4	AC4	SOFTWARE	GLU A:54 , TYR A:61 , LEU A:211 , GLN A:214	BINDING SITE FOR RESIDUE LIO A 1999

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

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

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

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.	CATA_ACIAD	136-164	2	A:136-164 B:136-164

(no "Exon" information available for 1DLM)

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:309
 aligned with CATA_ACIAD | P07773 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:309
                                    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       262       272       282       292       302         
           CATA_ACIAD     3 VKIFNTQDVQDFLRVASGLEQEGGNPRVKQIIHRVLSDLYKAIEDLNITSDEYWAGVAYLNQLGANQEAGLLSPGLGFDHYLDMRMDAEDAALGIENATPRTIEGPLYVAGAPESVGYARMDDGSDPNGHTLILHGTIFDADGKPLPNAKVEIWHANTKGFYSHFDPTGEQQAFNMRRSIITDENGQYRVRTILPAGYGCPPEGPTQQLLNQLGRHGNRPAHIHYFVSADGHRKLTTQINVAGDPYTYDDFAYATREGLVVDAVEHTDPEAIKANDVEGPFAEMVFDLKLTRLVDGVDNQVVDRPRLAV 311
               SCOP domains d1dlma_ A: Catechol 1,2-dioxygenase                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1dlmA00 A:3-311 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...............ee...eee.eee..........eeeeeeeee..........eeeee......................eeeee.....eeeeeee....ee....hhhhhhhhhh....ee..eeeeeee......eeeeeee..................ee..eee.hhhhhhhh.....eeeee..ee.................ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dlm A   3 VKIFNTQDVQDFLRVASGLEQEGGNPRVKQIIHRVLSDLYKAIEDLNITSDEYWAGVAYLNQLGANQEAGLLSPGLGFDHYLDMRMDAEDAALGIENATPRTIEGPLYVAGAPESVGYARMDDGSDPNGHTLILHGTIFDADGKPLPNAKVEIWHANTKGFYSHFDPTGEQQAFNMRRSIITDENGQYRVRTILPAGYGCPPEGPTQQLLNQLGRHGNRPAHIHYFVSADGHRKLTTQINVAGDPYTYDDFAYATREGLVVDAVEHTDPEAIKANDVEGPFAEMVFDLKLTRLVDGVDNQVVDRPRLAV 311
                                    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       262       272       282       292       302

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with CATA_ACIAD | P07773 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:309
                                    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       262       272       282       292       302         
           CATA_ACIAD     3 VKIFNTQDVQDFLRVASGLEQEGGNPRVKQIIHRVLSDLYKAIEDLNITSDEYWAGVAYLNQLGANQEAGLLSPGLGFDHYLDMRMDAEDAALGIENATPRTIEGPLYVAGAPESVGYARMDDGSDPNGHTLILHGTIFDADGKPLPNAKVEIWHANTKGFYSHFDPTGEQQAFNMRRSIITDENGQYRVRTILPAGYGCPPEGPTQQLLNQLGRHGNRPAHIHYFVSADGHRKLTTQINVAGDPYTYDDFAYATREGLVVDAVEHTDPEAIKANDVEGPFAEMVFDLKLTRLVDGVDNQVVDRPRLAV 311
               SCOP domains d1dlmb_ B: Catechol 1,2-dioxygenase                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1dlmB00 B:3-311 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..............ee...eee.eee..........eeeeeeeee..........eeeee......................eeeee.....eeeeeee....ee....hhhhhhhhhh....ee..eeeeeee......eeeeeee..................ee..eee.hhhhhhhh.....eeeee..ee.................ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dlm B   3 VKIFNTQDVQDFLRVASGLEQEGGNPRVKQIIHRVLSDLYKAIEDLNITSDEYWAGVAYLNQLGANQEAGLLSPGLGFDHYLDMRMDAEDAALGIENATPRTIEGPLYVAGAPESVGYARMDDGSDPNGHTLILHGTIFDADGKPLPNAKVEIWHANTKGFYSHFDPTGEQQAFNMRRSIITDENGQYRVRTILPAGYGCPPEGPTQQLLNQLGRHGNRPAHIHYFVSADGHRKLTTQINVAGDPYTYDDFAYATREGLVVDAVEHTDPEAIKANDVEGPFAEMVFDLKLTRLVDGVDNQVVDRPRLAV 311
                                    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       262       272       282       292       302

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Prealbumin-like (433)

Superfamily: Aromatic compound dioxygenase (111)

Family: Aromatic compound dioxygenase (100)

Protein domain: Catechol 1,2-dioxygenase (4)

Acinetobacter calcoaceticus [TaxId: 471] (4)

1a	d1dlma_	A:
1b	d1dlmb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Protocatechuate 3,4-Dioxygenase, subunit A (43)

Homologous Superfamily: Protocatechuate 3,4-Dioxygenase, subunit A (43)

Adp1 (Acinetobacter sp) (10)

1a	1dlmA00	A:3-311
1b	1dlmB00	B:3-311

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CATA_ACIAD | P07773)

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:0042952	beta-ketoadipate pathway	A pathway of aromatic compound degradation by ortho-cleavage; one branch converts protocatechuate, derived from phenolic compounds, to beta-ketoadipate, and the other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates.
	GO:0019614	catechol-containing compound catabolic process	The chemical reactions and pathways resulting in the breakdown of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent.
	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.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 1dlm)

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UniProtKB/Swiss-Prot
	CATA_ACIAD \| P07773	:	1dlq 1dlt 1dmh

1dlm	CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 NATIVE STRUCTURE
1dlq	CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 INHIBITED BY MERCURY
1dlt	CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND CATECHOL
1dmh	CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND 4-METHYLCATECHOL

Description

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Ligands, Modified Residues, Ions (2, 4)

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