1lo7: Difference between revisions

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X-ray structure of 4-Hydroxybenzoyl CoA Thioesterase complexed with 4-hydroxyphenacyl CoA

OverviewOverview

The metabolic pathway by which 4-chlorobenzoate is degraded to 4-hydroxybenzoate in the soil-dwelling microbe Pseudomonas sp. strain CBS-3 consists of three enzymes including 4-hydroxybenzoyl-CoA thioesterase. The structure of the unbound form of this thioesterase has been shown to contain the so-called "hot dog" fold with a large helix packed against a five-stranded anti-parallel beta-sheet. To address the manner in which the enzyme accommodates the substrate within the active site, two inhibitors have been synthesized, namely 4-hydroxyphenacyl-CoA and 4-hydroxybenzyl-CoA. Here we describe the structural analyses of the enzyme complexed with these two inhibitors determined and refined to 1.5 and 1.8 A resolution, respectively. These studies indicate that only one protein side chain, Ser(91), participates directly in ligand binding. All of the other interactions between the protein and the inhibitors are mediated through backbone peptidic NH groups, carbonyl oxygens, and/or solvents. The structures of the enzyme-inhibitor complexes suggest that both a hydrogen bond and the positive end of a helix dipole moment serve to polarize the electrons away from the carbonyl carbon of the acyl group, thereby making it more susceptible to nucleophilic attack. Additionally, these studies demonstrate that the carboxylate group of Asp(17) is approximately 3.2 A from the carbonyl carbon of the acyl group. To address the role of Asp(17), the structure of the site-directed mutant protein D17N with bound substrate has also been determined. Taken together, these investigations suggest that the reaction mechanism may proceed through an acyl enzyme intermediate.

About this StructureAbout this Structure

1LO7 is a Single protein structure of sequence from Pseudomonas sp. with and as ligands. Active as 4-hydroxybenzoyl-CoA thioesterase, with EC number 3.1.2.23 Full crystallographic information is available from OCA.

ReferenceReference

X-ray crystallographic analyses of inhibitor and substrate complexes of wild-type and mutant 4-hydroxybenzoyl-CoA thioesterase., Thoden JB, Holden HM, Zhuang Z, Dunaway-Mariano D, J Biol Chem. 2002 Jul 26;277(30):27468-76. Epub 2002 May 7. PMID:11997398

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-[[Image:1lo7.jpg|left|200px]]<br /><applet load="1lo7" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1lo7.jpg|left|200px]]<br /><applet load="1lo7" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1lo7, resolution 1.50&Aring;" />
 '''X-ray structure of 4-Hydroxybenzoyl CoA Thioesterase complexed with 4-hydroxyphenacyl CoA'''<br />
 ==Overview==
-The metabolic pathway by which 4-chlorobenzoate is degraded to, 4-hydroxybenzoate in the soil-dwelling microbe Pseudomonas sp. strain, CBS-3 consists of three enzymes including 4-hydroxybenzoyl-CoA, thioesterase. The structure of the unbound form of this thioesterase has, been shown to contain the so-called "hot dog" fold with a large helix, packed against a five-stranded anti-parallel beta-sheet. To address the, manner in which the enzyme accommodates the substrate within the active, site, two inhibitors have been synthesized, namely 4-hydroxyphenacyl-CoA, and 4-hydroxybenzyl-CoA. Here we describe the structural analyses of the, enzyme complexed with these two inhibitors determined and refined to 1.5, and 1.8 A resolution, respectively. These studies indicate that only one, protein side chain, Ser(91), participates directly in ligand binding. All, of the other interactions between the protein and the inhibitors are, mediated through backbone peptidic NH groups, carbonyl oxygens, and/or, solvents. The structures of the enzyme-inhibitor complexes suggest that, both a hydrogen bond and the positive end of a helix dipole moment serve, to polarize the electrons away from the carbonyl carbon of the acyl group, thereby making it more susceptible to nucleophilic attack. Additionally, these studies demonstrate that the carboxylate group of Asp(17) is, approximately 3.2 A from the carbonyl carbon of the acyl group. To address, the role of Asp(17), the structure of the site-directed mutant protein, D17N with bound substrate has also been determined. Taken together, these, investigations suggest that the reaction mechanism may proceed through an, acyl enzyme intermediate.
+The metabolic pathway by which 4-chlorobenzoate is degraded to 4-hydroxybenzoate in the soil-dwelling microbe Pseudomonas sp. strain CBS-3 consists of three enzymes including 4-hydroxybenzoyl-CoA thioesterase. The structure of the unbound form of this thioesterase has been shown to contain the so-called "hot dog" fold with a large helix packed against a five-stranded anti-parallel beta-sheet. To address the manner in which the enzyme accommodates the substrate within the active site, two inhibitors have been synthesized, namely 4-hydroxyphenacyl-CoA and 4-hydroxybenzyl-CoA. Here we describe the structural analyses of the enzyme complexed with these two inhibitors determined and refined to 1.5 and 1.8 A resolution, respectively. These studies indicate that only one protein side chain, Ser(91), participates directly in ligand binding. All of the other interactions between the protein and the inhibitors are mediated through backbone peptidic NH groups, carbonyl oxygens, and/or solvents. The structures of the enzyme-inhibitor complexes suggest that both a hydrogen bond and the positive end of a helix dipole moment serve to polarize the electrons away from the carbonyl carbon of the acyl group, thereby making it more susceptible to nucleophilic attack. Additionally, these studies demonstrate that the carboxylate group of Asp(17) is approximately 3.2 A from the carbonyl carbon of the acyl group. To address the role of Asp(17), the structure of the site-directed mutant protein D17N with bound substrate has also been determined. Taken together, these investigations suggest that the reaction mechanism may proceed through an acyl enzyme intermediate.
 ==About this Structure==
-LO7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.] with 4CO and EDO as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/4-hydroxybenzoyl-CoA_thioesterase 4-hydroxybenzoyl-CoA thioesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.2.23 3.1.2.23] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LO7 OCA].
+LO7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.] with <scene name='pdbligand=4CO:'>4CO</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/4-hydroxybenzoyl-CoA_thioesterase 4-hydroxybenzoyl-CoA thioesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.2.23 3.1.2.23] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LO7 OCA].
 ==Reference==
@@ Line 15: / Line 15: @@
 [[Category: Single protein]]
 [[Category: Dunaway-Mariano, D.]]
-[[Category: Holden, H.M.]]
+[[Category: Holden, H M.]]
-[[Category: Thoden, J.B.]]
+[[Category: Thoden, J B.]]
 [[Category: Zhuang, Z.]]
 [[Category: 4CO]]
@@ Line 24: / Line 24: @@
 [[Category: thioesterase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:42:42 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:46:45 2008''