1b4u: Difference between revisions
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[[Image:1b4u.gif|left|200px]] | [[Image:1b4u.gif|left|200px]] | ||
'''PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)''' | {{Structure | ||
|PDB= 1b4u |SIZE=350|CAPTION= <scene name='initialview01'>1b4u</scene>, resolution 2.2Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene> and <scene name='pdbligand=DHB:3,4-DIHYDROXYBENZOIC ACID'>DHB</scene> | |||
|ACTIVITY= [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] | |||
|GENE= | |||
}} | |||
'''PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1B4U is a [ | 1B4U is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4U OCA]. | ||
==Reference== | ==Reference== | ||
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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/10467151 10467151] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Protocatechuate 4,5-dioxygenase]] | [[Category: Protocatechuate 4,5-dioxygenase]] | ||
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[[Category: protocatechuate]] | [[Category: protocatechuate]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:06:15 2008'' | ||
Revision as of 11:06, 20 March 2008
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| , resolution 2.2Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Activity: | Protocatechuate 4,5-dioxygenase, with EC number 1.13.11.8 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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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