2d2x
From Proteopedia
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[[Image:2d2x.jpg|left|200px]] | [[Image:2d2x.jpg|left|200px]] | ||
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| - | | | + | {{STRUCTURE_2d2x| PDB=2d2x | SCENE= }} |
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'''Crystal structure of 2-deoxy-scyllo-inosose synthase''' | '''Crystal structure of 2-deoxy-scyllo-inosose synthase''' | ||
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| + | ==Overview== | ||
| + | A key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction. This reaction mechanism is similar to the catalysis by dehydroquinate synthase (DHQS) of the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate in the shikimate pathway, but significant dissimilarity between these enzymes is also known, particularly in the stereochemistry of the phosphate elimination reaction and the cyclization. Here, the crystal structures of DOIS from Bacillus circulans and its complex with the substrate analog inhibitor carbaglucose-6-phosphate, NAD+, and Co2+ have been determined to provide structural insights into the reaction mechanism. The complex structure shows that an active site exists between the N-terminal and C-terminal domains and that the inhibitor coordinates a cobalt ion in this site. Two subunits exist as a dimer in the asymmetric unit. The two active sites of the dimer were observed to be different. One contains a dephosphorylated compound derived from the inhibitor and the other includes the inhibitor without change. The present study suggested that phosphate elimination proceeds through syn-elimination assisted by Glu 243 and the aldol condensation proceeds via a boat conformation. Also discussed are significant similarities and dissimilarities between DOIS and DHQS, particularly in terms of the structure at the active site and the reaction mechanism. | ||
==About this Structure== | ==About this Structure== | ||
2D2X is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_circulans Bacillus circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2X OCA]. | 2D2X is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_circulans Bacillus circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2X OCA]. | ||
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| + | ==Reference== | ||
| + | Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+., Nango E, Kumasaka T, Hirayama T, Tanaka N, Eguchi T, Proteins. 2008 Feb 1;70(2):517-27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17879343 17879343] | ||
[[Category: Bacillus circulans]] | [[Category: Bacillus circulans]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: Tanaka, N.]] | [[Category: Tanaka, N.]] | ||
[[Category: 2-deoxystreptamine]] | [[Category: 2-deoxystreptamine]] | ||
| - | [[Category: | + | [[Category: Aminoglycoside]] |
| - | [[Category: | + | [[Category: Dehydroquinate synthase]] |
| - | + | [[Category: Lyase]] | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 30 13:23:55 2008'' |
Revision as of 10:23, 30 April 2008
Crystal structure of 2-deoxy-scyllo-inosose synthase
Overview
A key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction. This reaction mechanism is similar to the catalysis by dehydroquinate synthase (DHQS) of the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate in the shikimate pathway, but significant dissimilarity between these enzymes is also known, particularly in the stereochemistry of the phosphate elimination reaction and the cyclization. Here, the crystal structures of DOIS from Bacillus circulans and its complex with the substrate analog inhibitor carbaglucose-6-phosphate, NAD+, and Co2+ have been determined to provide structural insights into the reaction mechanism. The complex structure shows that an active site exists between the N-terminal and C-terminal domains and that the inhibitor coordinates a cobalt ion in this site. Two subunits exist as a dimer in the asymmetric unit. The two active sites of the dimer were observed to be different. One contains a dephosphorylated compound derived from the inhibitor and the other includes the inhibitor without change. The present study suggested that phosphate elimination proceeds through syn-elimination assisted by Glu 243 and the aldol condensation proceeds via a boat conformation. Also discussed are significant similarities and dissimilarities between DOIS and DHQS, particularly in terms of the structure at the active site and the reaction mechanism.
About this Structure
2D2X is a Single protein structure of sequence from Bacillus circulans. Full crystallographic information is available from OCA.
Reference
Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+., Nango E, Kumasaka T, Hirayama T, Tanaka N, Eguchi T, Proteins. 2008 Feb 1;70(2):517-27. PMID:17879343 Page seeded by OCA on Wed Apr 30 13:23:55 2008
