1jcy
From Proteopedia
(New page: 200px<br /><applet load="1jcy" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jcy, resolution 1.90Å" /> '''Aquifex aeolicus KDO...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1jcy.gif|left|200px]]<br /><applet load="1jcy" size=" | + | [[Image:1jcy.gif|left|200px]]<br /><applet load="1jcy" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1jcy, resolution 1.90Å" /> | caption="1jcy, resolution 1.90Å" /> | ||
'''Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium'''<br /> | '''Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We have determined the crystal structures of the metalloenzyme | + | We have determined the crystal structures of the metalloenzyme 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase from Aquifex aeolicus in complex with phosphoenolpyruvate (PEP) and ribose 5-phosphate (R5P), and with a bisubstrate inhibitor that mimics the postulated linear reaction intermediate. R5P, which is not a substrate for KDO8P synthase, binds in a manner similar to that of arabinose 5-phosphate (A5P), which is the natural substrate. The lack of reactivity of R5P appears to be primarily a consequence of the loss of a water molecule coordinated to Cd(2+) and located on the si side of PEP. This water molecule is no longer present because it cannot form a hydrogen bond with C2-OH(R5P), which is oriented in a different direction from C2-OH(A5P). The bisubstrate inhibitor binds with its phosphate and phosphonate moieties occupying the positions of the phosphate groups of A5P and PEP, respectively. One of the inhibitor hydroxyls replaces water as a ligand of Cd(2+). The current work supports a mechanism for the synthesis of KDO8P, in which a hydroxide ion on the si side of PEP attacks C2(PEP), forming a tetrahedral-like intermediate with a buildup of negative charge at C3(PEP). The ensuing condensation of C3(PEP) with C1(A5P) would be favored by a proton transfer from the phosphate moiety of PEP to the aldehyde carbonyl of A5P to generate the hydroxyl. Overall, the process can be described as a syn addition of water and A5P to the si side of PEP. |
==About this Structure== | ==About this Structure== | ||
| - | 1JCY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with R5P, CD, PO4 and PEP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] Full crystallographic information is available from [http:// | + | 1JCY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with <scene name='pdbligand=R5P:'>R5P</scene>, <scene name='pdbligand=CD:'>CD</scene>, <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=PEP:'>PEP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JCY OCA]. |
==Reference== | ==Reference== | ||
| Line 14: | Line 14: | ||
[[Category: Aquifex aeolicus]] | [[Category: Aquifex aeolicus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Duewel, H | + | [[Category: Duewel, H S.]] |
| - | [[Category: Gatti, D | + | [[Category: Gatti, D L.]] |
[[Category: Wang, J.]] | [[Category: Wang, J.]] | ||
| - | [[Category: Woodard, R | + | [[Category: Woodard, R W.]] |
[[Category: CD]] | [[Category: CD]] | ||
[[Category: PEP]] | [[Category: PEP]] | ||
| Line 29: | Line 29: | ||
[[Category: r5p]] | [[Category: r5p]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:21:13 2008'' |
Revision as of 11:21, 21 February 2008
|
Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium
Overview
We have determined the crystal structures of the metalloenzyme 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase from Aquifex aeolicus in complex with phosphoenolpyruvate (PEP) and ribose 5-phosphate (R5P), and with a bisubstrate inhibitor that mimics the postulated linear reaction intermediate. R5P, which is not a substrate for KDO8P synthase, binds in a manner similar to that of arabinose 5-phosphate (A5P), which is the natural substrate. The lack of reactivity of R5P appears to be primarily a consequence of the loss of a water molecule coordinated to Cd(2+) and located on the si side of PEP. This water molecule is no longer present because it cannot form a hydrogen bond with C2-OH(R5P), which is oriented in a different direction from C2-OH(A5P). The bisubstrate inhibitor binds with its phosphate and phosphonate moieties occupying the positions of the phosphate groups of A5P and PEP, respectively. One of the inhibitor hydroxyls replaces water as a ligand of Cd(2+). The current work supports a mechanism for the synthesis of KDO8P, in which a hydroxide ion on the si side of PEP attacks C2(PEP), forming a tetrahedral-like intermediate with a buildup of negative charge at C3(PEP). The ensuing condensation of C3(PEP) with C1(A5P) would be favored by a proton transfer from the phosphate moiety of PEP to the aldehyde carbonyl of A5P to generate the hydroxyl. Overall, the process can be described as a syn addition of water and A5P to the si side of PEP.
About this Structure
1JCY is a Single protein structure of sequence from Aquifex aeolicus with , , and as ligands. Active as 3-deoxy-8-phosphooctulonate synthase, with EC number 2.5.1.55 Full crystallographic information is available from OCA.
Reference
Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis., Wang J, Duewel HS, Woodard RW, Gatti DL, Biochemistry. 2001 Dec 25;40(51):15676-83. PMID:11747443
Page seeded by OCA on Thu Feb 21 13:21:13 2008
Categories: 3-deoxy-8-phosphooctulonate synthase | Aquifex aeolicus | Single protein | Duewel, H S. | Gatti, D L. | Wang, J. | Woodard, R W. | CD | PEP | PO4 | R5P | Beta/alpha barrel | Kdo | Kdo8p | Kdo8ps | Pep | R5p
