1b4u: Difference between revisions

Revision as of 12:51, 21 February 2008

PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)

OverviewOverview

BACKGROUND: Sphingomonas paucimobilis SYK-6 utilizes an extradiol-type catecholic dioxygenase, the LigAB enzyme (a protocatechuate 4,5-dioxygenase), to oxidize protocatechuate (or 3,4-dihydroxybenzoic acid, PCA). The enzyme belongs to the family of class III extradiol-type catecholic dioxygenases catalyzing the ring-opening reaction of protocatechuate and related compounds. The primary structure of LigAB suggests that the enzyme has no evolutionary relationship with the family of class II extradiol-type catecholic dioxygenases. Both the class II and class III enzymes utilize a non-heme ferrous center for adding dioxygen to the substrate. By elucidating the structure of LigAB, we aimed to provide a structural basis for discussing the function of class III enzymes. RESULTS: The crystal structure of substrate-free LigAB was solved at 2.2 A resolution. The molecule is an alpha2beta2 tetramer. The active site contains a non-heme iron coordinated by His12, His61, Glu242, and a water molecule located in a deep cleft of the beta subunit, which is covered by the alpha subunit. Because of the apparent oxidation of the Fe ion into the nonphysiological Fe(III) state, we could also solve the structure of LigAB complexed with a substrate, PCA. The iron coordination sphere in this complex is a distorted tetragonal bipyramid with one ligand missing, which is presumed to be the O2-binding site. CONCLUSIONS: The structure of LigAB is completely different from those of the class II extradiol-type dioxygenases exemplified by the BphC enzyme, a 2,3-dihydroxybiphenyl 1,2-dioxygenase from a Pseudomonas species. Thus, as already implicated by the primary structures, no evolutionary relationship exists between the class II and III enzymes. However, the two classes of enzymes share many geometrical characteristics with respect to the nature of the iron coordination sphere and the position of a putative catalytic base, strongly suggesting a common catalytic mechanism.

About this StructureAbout this Structure

1B4U is a Protein complex structure of sequences from Sphingomonas paucimobilis with and as ligands. Active as Protocatechuate 4,5-dioxygenase, with EC number 1.13.11.8 Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions., Sugimoto K, Senda T, Aoshima H, Masai E, Fukuda M, Mitsui Y, Structure. 1999 Aug 15;7(8):953-65. PMID:10467151

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-[[Image:1b4u.gif|left|200px]]<br /><applet load="1b4u" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1b4u.gif|left|200px]]<br /><applet load="1b4u" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1b4u, resolution 2.2&Aring;" />
 '''PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)'''<br />
 ==Overview==
-BACKGROUND: Sphingomonas paucimobilis SYK-6 utilizes an extradiol-type, catecholic dioxygenase, the LigAB enzyme (a protocatechuate, 4,5-dioxygenase), to oxidize protocatechuate (or 3,4-dihydroxybenzoic, acid, PCA). The enzyme belongs to the family of class III extradiol-type, catecholic dioxygenases catalyzing the ring-opening reaction of, protocatechuate and related compounds. The primary structure of LigAB, suggests that the enzyme has no evolutionary relationship with the family, of class II extradiol-type catecholic dioxygenases. Both the class II and, class III enzymes utilize a non-heme ferrous center for adding dioxygen to, the substrate. By elucidating the structure of LigAB, we aimed to provide, a structural basis for discussing the function of class III enzymes., RESULTS: The crystal structure of substrate-free LigAB was solved at 2.2 A, resolution. The molecule is an alpha2beta2 tetramer. The active site, contains a non-heme iron coordinated by His12, His61, Glu242, and a water, molecule located in a deep cleft of the beta subunit, which is covered by, the alpha subunit. Because of the apparent oxidation of the Fe ion into, the nonphysiological Fe(III) state, we could also solve the structure of, LigAB complexed with a substrate, PCA. The iron coordination sphere in, this complex is a distorted tetragonal bipyramid with one ligand missing, which is presumed to be the O2-binding site. CONCLUSIONS: The structure of, LigAB is completely different from those of the class II extradiol-type, dioxygenases exemplified by the BphC enzyme, a 2,3-dihydroxybiphenyl, 1,2-dioxygenase from a Pseudomonas species. Thus, as already implicated by, the primary structures, no evolutionary relationship exists between the, class II and III enzymes. However, the two classes of enzymes share many, geometrical characteristics with respect to the nature of the iron, coordination sphere and the position of a putative catalytic base, strongly suggesting a common catalytic mechanism.
+BACKGROUND: Sphingomonas paucimobilis SYK-6 utilizes an extradiol-type catecholic dioxygenase, the LigAB enzyme (a protocatechuate 4,5-dioxygenase), to oxidize protocatechuate (or 3,4-dihydroxybenzoic acid, PCA). The enzyme belongs to the family of class III extradiol-type catecholic dioxygenases catalyzing the ring-opening reaction of protocatechuate and related compounds. The primary structure of LigAB suggests that the enzyme has no evolutionary relationship with the family of class II extradiol-type catecholic dioxygenases. Both the class II and class III enzymes utilize a non-heme ferrous center for adding dioxygen to the substrate. By elucidating the structure of LigAB, we aimed to provide a structural basis for discussing the function of class III enzymes. RESULTS: The crystal structure of substrate-free LigAB was solved at 2.2 A resolution. The molecule is an alpha2beta2 tetramer. The active site contains a non-heme iron coordinated by His12, His61, Glu242, and a water molecule located in a deep cleft of the beta subunit, which is covered by the alpha subunit. Because of the apparent oxidation of the Fe ion into the nonphysiological Fe(III) state, we could also solve the structure of LigAB complexed with a substrate, PCA. The iron coordination sphere in this complex is a distorted tetragonal bipyramid with one ligand missing, which is presumed to be the O2-binding site. CONCLUSIONS: The structure of LigAB is completely different from those of the class II extradiol-type dioxygenases exemplified by the BphC enzyme, a 2,3-dihydroxybiphenyl 1,2-dioxygenase from a Pseudomonas species. Thus, as already implicated by the primary structures, no evolutionary relationship exists between the class II and III enzymes. However, the two classes of enzymes share many geometrical characteristics with respect to the nature of the iron coordination sphere and the position of a putative catalytic base, strongly suggesting a common catalytic mechanism.
 ==About this Structure==
-B4U is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis] with FE and DHB as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Protocatechuate_4,5-dioxygenase Protocatechuate 4,5-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.8 1.13.11.8] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1B4U OCA].
+B4U is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=DHB:'>DHB</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Protocatechuate_4,5-dioxygenase Protocatechuate 4,5-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.8 1.13.11.8] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4U OCA].
 ==Reference==
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 [[Category: protocatechuate]]
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