2ddh
From Proteopedia
(New page: 200px<br /><applet load="2ddh" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ddh, resolution 2.070Å" /> '''Crystal Structure o...) |
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| - | [[Image:2ddh.gif|left|200px]]<br /><applet load="2ddh" size=" | + | [[Image:2ddh.gif|left|200px]]<br /><applet load="2ddh" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2ddh, resolution 2.070Å" /> | caption="2ddh, resolution 2.070Å" /> | ||
'''Crystal Structure of Acyl-CoA oxidase complexed with 3-OH-dodecanoate'''<br /> | '''Crystal Structure of Acyl-CoA oxidase complexed with 3-OH-dodecanoate'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The three-dimensional structure of rat-liver acyl-CoA oxidase-II (ACO-II) | + | The three-dimensional structure of rat-liver acyl-CoA oxidase-II (ACO-II) in a complex with a C12-fatty acid was solved by the molecular replacement method based on the uncomplexed ACO-II structure. The crystalline form of the complex was obtained by cocrystallization of ACO-II with dodecanoyl-CoA. The crystalline complex possessed, in the active-site crevice, only the fatty acid moiety that had been formed through hydrolysis of the thioester bond. The overall dimeric structure and the folding pattern of each subunit are essentially superimposable on those of uncomplexed ACO-II. The active site including the flavin ring of FAD, the crevice embracing the fatty acyl moiety, and adjacent amino acid side chains are superimposably conserved with the exception of Glu421, whose carboxylate group is tilted away to accommodate the fatty acid. One of the carboxyl oxygens of the bound fatty acid is hydrogen-bonded to the amide hydrogen of Glu421, the presumed catalytic base, and to the ribityl 2'-hydroxyl group of FAD. This hydrogen-bonding network correlates well with the substrate recognition/activation in acyl-CoA dehydrogenase. The binding mode of C12-fatty acid suggests that the active site does not close upon substrate binding, but remains spacious during the entire catalytic process, the oxygen accessibility in the oxidative half-reaction thereby being maintained. |
==About this Structure== | ==About this Structure== | ||
| - | 2DDH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with FAD and HXD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Acyl-CoA_oxidase Acyl-CoA oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.6 1.3.3.6] Full crystallographic information is available from [http:// | + | 2DDH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with <scene name='pdbligand=FAD:'>FAD</scene> and <scene name='pdbligand=HXD:'>HXD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Acyl-CoA_oxidase Acyl-CoA oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.6 1.3.3.6] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDH OCA]. |
==Reference== | ==Reference== | ||
| - | Three-dimensional structure of rat-liver acyl-CoA oxidase in complex with a fatty acid: insights into substrate-recognition and reactivity toward molecular oxygen., Tokuoka K, Nakajima Y, Hirotsu K, Miyahara I, Nishina Y, Shiga K, Tamaoki H, Setoyama C, Tojo H, Miura R, J Biochem | + | Three-dimensional structure of rat-liver acyl-CoA oxidase in complex with a fatty acid: insights into substrate-recognition and reactivity toward molecular oxygen., Tokuoka K, Nakajima Y, Hirotsu K, Miyahara I, Nishina Y, Shiga K, Tamaoki H, Setoyama C, Tojo H, Miura R, J Biochem. 2006 Apr;139(4):789-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16672280 16672280] |
[[Category: Acyl-CoA oxidase]] | [[Category: Acyl-CoA oxidase]] | ||
[[Category: Rattus norvegicus]] | [[Category: Rattus norvegicus]] | ||
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[[Category: beta barrel]] | [[Category: beta barrel]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:57:41 2008'' |
Revision as of 14:57, 21 February 2008
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Crystal Structure of Acyl-CoA oxidase complexed with 3-OH-dodecanoate
Overview
The three-dimensional structure of rat-liver acyl-CoA oxidase-II (ACO-II) in a complex with a C12-fatty acid was solved by the molecular replacement method based on the uncomplexed ACO-II structure. The crystalline form of the complex was obtained by cocrystallization of ACO-II with dodecanoyl-CoA. The crystalline complex possessed, in the active-site crevice, only the fatty acid moiety that had been formed through hydrolysis of the thioester bond. The overall dimeric structure and the folding pattern of each subunit are essentially superimposable on those of uncomplexed ACO-II. The active site including the flavin ring of FAD, the crevice embracing the fatty acyl moiety, and adjacent amino acid side chains are superimposably conserved with the exception of Glu421, whose carboxylate group is tilted away to accommodate the fatty acid. One of the carboxyl oxygens of the bound fatty acid is hydrogen-bonded to the amide hydrogen of Glu421, the presumed catalytic base, and to the ribityl 2'-hydroxyl group of FAD. This hydrogen-bonding network correlates well with the substrate recognition/activation in acyl-CoA dehydrogenase. The binding mode of C12-fatty acid suggests that the active site does not close upon substrate binding, but remains spacious during the entire catalytic process, the oxygen accessibility in the oxidative half-reaction thereby being maintained.
About this Structure
2DDH is a Single protein structure of sequence from Rattus norvegicus with and as ligands. Active as Acyl-CoA oxidase, with EC number 1.3.3.6 Full crystallographic information is available from OCA.
Reference
Three-dimensional structure of rat-liver acyl-CoA oxidase in complex with a fatty acid: insights into substrate-recognition and reactivity toward molecular oxygen., Tokuoka K, Nakajima Y, Hirotsu K, Miyahara I, Nishina Y, Shiga K, Tamaoki H, Setoyama C, Tojo H, Miura R, J Biochem. 2006 Apr;139(4):789-95. PMID:16672280
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