1k4i
From Proteopedia
(New page: 200px<br /><applet load="1k4i" size="450" color="white" frame="true" align="right" spinBox="true" caption="1k4i, resolution 0.98Å" /> '''Crystal Structure of...) |
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| - | [[Image:1k4i.jpg|left|200px]]<br /><applet load="1k4i" size=" | + | [[Image:1k4i.jpg|left|200px]]<br /><applet load="1k4i" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1k4i, resolution 0.98Å" /> | caption="1k4i, resolution 0.98Å" /> | ||
'''Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with two Magnesium ions'''<br /> | '''Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with two Magnesium ions'''<br /> | ||
==Overview== | ==Overview== | ||
| - | X-ray crystal structures of L-3,4-dihydroxy-2-butanone-4-phosphate | + | X-ray crystal structures of L-3,4-dihydroxy-2-butanone-4-phosphate synthase from Magnaporthe grisea are reported for the E-SO(4)(2-), E-SO(4)(2-)-Mg(2+), E-SO(4)(2)(-)-Mn(2+), E-SO(4)(2)(-)-Mn(2+)-glycerol, and E-SO(4)(2)(-)-Zn(2+) complexes with resolutions that extend to 1.55, 0.98, 1.60, 1.16, and 1.00 A, respectively. Active-site residues of the homodimer are fully defined. The structures were used to model the substrate ribulose 5-phosphate in the active site with the phosphate group anchored at the sulfate site and the placement of the ribulose group guided by the glycerol site. The model includes two Mg(2+) cations that bind to the oxygen substituents of the C2, C3, C4, and phosphate groups of the substrate, the side chains of Glu37 and His153, and water molecules. The position of the metal cofactors and the substrate's phosphate group are further stabilized by an extensive hydrogen-bond and salt-bridge network. On the basis of their proximity to the substrate's reaction participants, the imidazole of an Asp99-His136 dyad from one subunit, the side chains of the Asp41, Cys66, and Glu174 residues from the other subunit, and Mg(2+)-activated water molecules are proposed to serve specific roles in the catalytic cycle as general acid-base functionalities. The model suggests that during the 1,2-shift step of the reaction, the substrate's C3 and C4 hydroxyl groups are cis to each other. A cis transition state is calculated to have an activation barrier that is 2 kcal/mol greater than that of the trans transition state in the absence of the enzyme. |
==About this Structure== | ==About this Structure== | ||
| - | 1K4I is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Magnaporthe_grisea Magnaporthe grisea] with SO4 and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1K4I is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Magnaporthe_grisea Magnaporthe grisea] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K4I OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Magnaporthe grisea]] | [[Category: Magnaporthe grisea]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Jordan, D | + | [[Category: Jordan, D B.]] |
| - | [[Category: Liao, D | + | [[Category: Liao, D I.]] |
| - | [[Category: Viitanen, P | + | [[Category: Viitanen, P V.]] |
| - | [[Category: Zheng, Y | + | [[Category: Zheng, Y J.]] |
[[Category: MG]] | [[Category: MG]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
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[[Category: structure-based design]] | [[Category: structure-based design]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:30:04 2008'' |
Revision as of 11:30, 21 February 2008
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Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with two Magnesium ions
Overview
X-ray crystal structures of L-3,4-dihydroxy-2-butanone-4-phosphate synthase from Magnaporthe grisea are reported for the E-SO(4)(2-), E-SO(4)(2-)-Mg(2+), E-SO(4)(2)(-)-Mn(2+), E-SO(4)(2)(-)-Mn(2+)-glycerol, and E-SO(4)(2)(-)-Zn(2+) complexes with resolutions that extend to 1.55, 0.98, 1.60, 1.16, and 1.00 A, respectively. Active-site residues of the homodimer are fully defined. The structures were used to model the substrate ribulose 5-phosphate in the active site with the phosphate group anchored at the sulfate site and the placement of the ribulose group guided by the glycerol site. The model includes two Mg(2+) cations that bind to the oxygen substituents of the C2, C3, C4, and phosphate groups of the substrate, the side chains of Glu37 and His153, and water molecules. The position of the metal cofactors and the substrate's phosphate group are further stabilized by an extensive hydrogen-bond and salt-bridge network. On the basis of their proximity to the substrate's reaction participants, the imidazole of an Asp99-His136 dyad from one subunit, the side chains of the Asp41, Cys66, and Glu174 residues from the other subunit, and Mg(2+)-activated water molecules are proposed to serve specific roles in the catalytic cycle as general acid-base functionalities. The model suggests that during the 1,2-shift step of the reaction, the substrate's C3 and C4 hydroxyl groups are cis to each other. A cis transition state is calculated to have an activation barrier that is 2 kcal/mol greater than that of the trans transition state in the absence of the enzyme.
About this Structure
1K4I is a Single protein structure of sequence from Magnaporthe grisea with and as ligands. Full crystallographic information is available from OCA.
Reference
Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase., Liao DI, Zheng YJ, Viitanen PV, Jordan DB, Biochemistry. 2002 Feb 12;41(6):1795-806. PMID:11827524
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