1jcy: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1jcy.gif|left|200px]] | [[Image:1jcy.gif|left|200px]] | ||
<!-- | |||
The line below this paragraph, containing "STRUCTURE_1jcy", creates the "Structure Box" on the page. | |||
You may change the PDB parameter (which sets the PDB file loaded into the applet) | |||
or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |||
or leave the SCENE parameter empty for the default display. | |||
| | --> | ||
| | {{STRUCTURE_1jcy| PDB=1jcy | SCENE= }} | ||
}} | |||
'''Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium''' | '''Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium''' | ||
| Line 30: | Line 27: | ||
[[Category: Wang, J.]] | [[Category: Wang, J.]] | ||
[[Category: Woodard, R W.]] | [[Category: Woodard, R W.]] | ||
[[Category: | [[Category: Beta/alpha barrel]] | ||
[[Category: | [[Category: Kdo]] | ||
[[Category: | [[Category: Kdo8p]] | ||
[[Category: | [[Category: Kdo8p]] | ||
[[Category: | [[Category: Pep]] | ||
[[Category: | [[Category: R5p]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 21:04:19 2008'' | |||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | |||
Revision as of 21:04, 2 May 2008
Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium
OverviewOverview
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 StructureAbout this Structure
1JCY is a Single protein structure of sequence from Aquifex aeolicus. Full crystallographic information is available from OCA.
ReferenceReference
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 Fri May 2 21:04:19 2008