1tmx: Difference between revisions

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Revision as of 15:20, 20 March 2008

File:1tmx.gif

, resolution 1.75Å

Ligands:

, , , , and

Activity:

Hydroxyquinol 1,2-dioxygenase, with EC number 1.13.11.37

Coordinates:

save as pdb, mmCIF, xml

Crystal structure of hydroxyquinol 1,2-dioxygenase from Nocardioides Simplex 3E

OverviewOverview

Hydroxyquinol 1,2-dioxygenase (1,2-HQD) catalyzes the ring cleavage of hydroxyquinol (1,2,4-trihydroxybenzene), a central intermediate in the degradation of aromatic compounds including a variety of particularly recalcitrant polychloro- and nitroaromatic pollutants. We report here the primary sequence determination and the analysis of the crystal structure of the 1,2-HQD from Nocardioides simplex 3E solved at 1.75 A resolution using the multiple wavelength anomalous dispersion of the two catalytic irons (1 Fe/293 amino acids). The catalytic Fe(III) coordination polyhedron composed by the side chains of Tyr164, Tyr197, His221, and His223 resembles that of the other known intradiol-cleaving dioxygenases, but several of the tertiary structure features are notably different. One of the most distinctive characteristics of the present structure is the extensive openings and consequent exposure to solvent of the upper part of the catalytic cavity arranged to favor the binding of hydroxyquinols but not catechols. A co-crystallized benzoate-like molecule is also found bound to the metal center forming a distinctive hydrogen bond network as observed previously also in 4-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP. This is the first structure of an intradiol dioxygenase specialized in hydroxyquinol ring cleavage to be investigated in detail.

About this StructureAbout this Structure

1TMX is a Single protein structure of sequence from Pimelobacter simplex. Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation., Ferraroni M, Seifert J, Travkin VM, Thiel M, Kaschabek S, Scozzafava A, Golovleva L, Schlomann M, Briganti F, J Biol Chem. 2005 Jun 3;280(22):21144-54. Epub 2005 Mar 16. PMID:15772073

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OCA

@@ Line 1: / Line 1: @@
-[[Image:1tmx.gif|left|200px]]<br /><applet load="1tmx" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1tmx.gif|left|200px]]
-caption="1tmx, resolution 1.75&Aring;" />
-'''Crystal structure of hydroxyquinol 1,2-dioxygenase from Nocardioides Simplex 3E'''<br />
+ {{Structure
+|PDB= 1tmx |SIZE=350|CAPTION= <scene name='initialview01'>1tmx</scene>, resolution 1.75&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=HGX:1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYL+CHOLINE'>HGX</scene> and <scene name='pdbligand=BEZ:BENZOIC ACID'>BEZ</scene>
+|ACTIVITY= [http://en.wikipedia.org/wiki/Hydroxyquinol_1,2-dioxygenase Hydroxyquinol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.37 1.13.11.37]
+|GENE=
+}}
+'''Crystal structure of hydroxyquinol 1,2-dioxygenase from Nocardioides Simplex 3E'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-TMX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pimelobacter_simplex Pimelobacter simplex] with <scene name='pdbligand=FE:'>FE</scene>, <scene name='pdbligand=CU:'>CU</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=HGX:'>HGX</scene> and <scene name='pdbligand=BEZ:'>BEZ</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Hydroxyquinol_1,2-dioxygenase Hydroxyquinol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.37 1.13.11.37] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMX OCA].
+TMX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pimelobacter_simplex Pimelobacter simplex]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMX OCA].
 ==Reference==
-Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation., Ferraroni M, Seifert J, Travkin VM, Thiel M, Kaschabek S, Scozzafava A, Golovleva L, Schlomann M, Briganti F, J Biol Chem. 2005 Jun 3;280(22):21144-54. Epub 2005 Mar 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15772073 15772073]
+Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation., Ferraroni M, Seifert J, Travkin VM, Thiel M, Kaschabek S, Scozzafava A, Golovleva L, Schlomann M, Briganti F, J Biol Chem. 2005 Jun 3;280(22):21144-54. Epub 2005 Mar 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15772073 15772073]
 [[Category: Hydroxyquinol 1,2-dioxygenase]]
 [[Category: Pimelobacter simplex]]
@@ Line 29: / Line 38: @@
 [[Category: beta barrel]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:15:16 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:20:30 2008''